diff --git a/source/blender/blenkernel/BKE_lib_id.h b/source/blender/blenkernel/BKE_lib_id.h
index ca734872502..a96791707e8 100644
--- a/source/blender/blenkernel/BKE_lib_id.h
+++ b/source/blender/blenkernel/BKE_lib_id.h
@@ -464,18 +464,27 @@ struct ID *BKE_id_copy_for_use_in_bmain(struct Main *bmain, const struct ID *id)
  * Does a mere memory swap over the whole IDs data (including type-specific memory).
  * \note Most internal ID data itself is not swapped (only IDProperties are).
  *
- * \param bmain: May be NULL, in which case there will be no remapping of internal pointers to
- * itself.
+ * \param bmain: May be NULL, in which case there is no guarantee that internal remapping of ID
+ * pointers to themselves will be complete (reguarding depsgraph and/or runtime data updates).
+ * \param do_self_remap: Whether to remap internal pointers to itself or not.
+ * \param self_remap_flags: Flags controlling self remapping, see BKE_lib_remap.h.
  */
-void BKE_lib_id_swap(struct Main *bmain, struct ID *id_a, struct ID *id_b);
+void BKE_lib_id_swap(struct Main *bmain,
+                     struct ID *id_a,
+                     struct ID *id_b,
+                     const bool do_self_remap,
+                     const int self_remap_flags);
 /**
  * Does a mere memory swap over the whole IDs data (including type-specific memory).
  * \note All internal ID data itself is also swapped.
  *
- * \param bmain: May be NULL, in which case there will be no remapping of internal pointers to
- * itself.
+ * For parameters description, see #BKE_lib_id_swap above.
  */
-void BKE_lib_id_swap_full(struct Main *bmain, struct ID *id_a, struct ID *id_b);
+void BKE_lib_id_swap_full(struct Main *bmain,
+                          struct ID *id_a,
+                          struct ID *id_b,
+                          const bool do_self_remap,
+                          const int self_remap_flags);
 
 /**
  * Sort given \a id into given \a lb list, using case-insensitive comparison of the id names.
diff --git a/source/blender/blenkernel/intern/brush.cc b/source/blender/blenkernel/intern/brush.cc
index b72f19abd8a..01652c7e2c3 100644
--- a/source/blender/blenkernel/intern/brush.cc
+++ b/source/blender/blenkernel/intern/brush.cc
@@ -416,7 +416,7 @@ static int brush_undo_preserve_cb(LibraryIDLinkCallbackData *cb_data)
 static void brush_undo_preserve(BlendLibReader *reader, ID *id_new, ID *id_old)
 {
   /* Whole Brush is preserved across undo-steps. */
-  BKE_lib_id_swap(nullptr, id_new, id_old);
+  BKE_lib_id_swap(nullptr, id_new, id_old, false, 0);
 
   /* `id_new` now has content from `id_old`, we need to ensure those old ID pointers are valid.
    * NOTE: Since we want to re-use all old pointers here, code is much simpler than for Scene. */
diff --git a/source/blender/blenkernel/intern/lib_id.c b/source/blender/blenkernel/intern/lib_id.c
index 0d9ff62a2ed..638aa6d9b7b 100644
--- a/source/blender/blenkernel/intern/lib_id.c
+++ b/source/blender/blenkernel/intern/lib_id.c
@@ -765,14 +765,38 @@ ID *BKE_id_copy_for_use_in_bmain(Main *bmain, const ID *id)
   return newid;
 }
 
+static void id_embedded_swap(ID **embedded_id_a,
+                             ID **embedded_id_b,
+                             const bool do_full_id,
+                             struct IDRemapper *remapper_id_a,
+                             struct IDRemapper *remapper_id_b);
+
 /**
  * Does a mere memory swap over the whole IDs data (including type-specific memory).
  * \note Most internal ID data itself is not swapped (only IDProperties are).
  */
-static void id_swap(Main *bmain, ID *id_a, ID *id_b, const bool do_full_id)
+static void id_swap(Main *bmain,
+                    ID *id_a,
+                    ID *id_b,
+                    const bool do_full_id,
+                    const bool do_self_remap,
+                    struct IDRemapper *input_remapper_id_a,
+                    struct IDRemapper *input_remapper_id_b,
+                    const int self_remap_flags)
 {
   BLI_assert(GS(id_a->name) == GS(id_b->name));
 
+  struct IDRemapper *remapper_id_a = input_remapper_id_a;
+  struct IDRemapper *remapper_id_b = input_remapper_id_b;
+  if (do_self_remap) {
+    if (remapper_id_a == NULL) {
+      remapper_id_a = BKE_id_remapper_create();
+    }
+    if (remapper_id_b == NULL) {
+      remapper_id_b = BKE_id_remapper_create();
+    }
+  }
+
   const IDTypeInfo *id_type = BKE_idtype_get_info_from_id(id_a);
   BLI_assert(id_type != NULL);
   const size_t id_struct_size = id_type->struct_size;
@@ -799,21 +823,87 @@ static void id_swap(Main *bmain, ID *id_a, ID *id_b, const bool do_full_id)
     id_b->recalc = id_a_back.recalc;
   }
 
-  if (bmain != NULL) {
-    /* Swap will have broken internal references to itself, restore them. */
-    BKE_libblock_relink_ex(bmain, id_a, id_b, id_a, ID_REMAP_SKIP_NEVER_NULL_USAGE);
-    BKE_libblock_relink_ex(bmain, id_b, id_a, id_b, ID_REMAP_SKIP_NEVER_NULL_USAGE);
+  id_embedded_swap((ID **)BKE_ntree_ptr_from_id(id_a),
+                   (ID **)BKE_ntree_ptr_from_id(id_b),
+                   do_full_id,
+                   remapper_id_a,
+                   remapper_id_b);
+  if (GS(id_a->name) == ID_SCE) {
+    Scene *scene_a = (Scene *)id_a;
+    Scene *scene_b = (Scene *)id_b;
+    id_embedded_swap((ID **)&scene_a->master_collection,
+                     (ID **)&scene_b->master_collection,
+                     do_full_id,
+                     remapper_id_a,
+                     remapper_id_b);
+  }
+
+  if (remapper_id_a != NULL) {
+    BKE_id_remapper_add(remapper_id_a, id_b, id_a);
+  }
+  if (remapper_id_b != NULL) {
+    BKE_id_remapper_add(remapper_id_b, id_a, id_b);
+  }
+
+  /* Finalize remapping of internal referrences to self broken by swapping, if requested. */
+  if (do_self_remap) {
+    LinkNode ids = {.next = NULL, .link = id_a};
+    BKE_libblock_relink_multiple(
+        bmain, &ids, ID_REMAP_TYPE_REMAP, remapper_id_a, self_remap_flags);
+    ids.link = id_b;
+    BKE_libblock_relink_multiple(
+        bmain, &ids, ID_REMAP_TYPE_REMAP, remapper_id_b, self_remap_flags);
+  }
+
+  if (input_remapper_id_a == NULL && remapper_id_a != NULL) {
+    BKE_id_remapper_free(remapper_id_a);
+  }
+  if (input_remapper_id_b == NULL && remapper_id_b != NULL) {
+    BKE_id_remapper_free(remapper_id_b);
   }
 }
 
-void BKE_lib_id_swap(Main *bmain, ID *id_a, ID *id_b)
+/* Conceptually, embedded IDs are part of their owner's data. However, some parts of the code
+ * (like e.g. the depsgraph) may treat them as independant IDs, so swapping them here and
+ * switching their pointers in the owner IDs allows to help not break cached relationships and
+ * such (by preserving the pointer values). */
+static void id_embedded_swap(ID **embedded_id_a,
+                             ID **embedded_id_b,
+                             const bool do_full_id,
+                             struct IDRemapper *remapper_id_a,
+                             struct IDRemapper *remapper_id_b)
 {
-  id_swap(bmain, id_a, id_b, false);
+  if (embedded_id_a != NULL && *embedded_id_a != NULL) {
+    BLI_assert(embedded_id_b != NULL && *embedded_id_b != NULL);
+
+    /* Do not remap internal references to itself here, since embedded IDs pointers also need to be
+     * potentially remapped in owner ID's data, which will also handle embedded IDs data. */
+    id_swap(
+        NULL, *embedded_id_a, *embedded_id_b, do_full_id, false, remapper_id_a, remapper_id_b, 0);
+    /* Manual 'remap' of owning embedded pointer in owner ID. */
+    SWAP(ID *, *embedded_id_a, *embedded_id_b);
+
+    /* Restore internal pointers to the swapped embedded IDs in their owners' data. This also
+     * includes the potential self-references inside the embedded IDs themselves. */
+    if (remapper_id_a != NULL) {
+      BKE_id_remapper_add(remapper_id_a, *embedded_id_b, *embedded_id_a);
+    }
+    if (remapper_id_b != NULL) {
+      BKE_id_remapper_add(remapper_id_b, *embedded_id_a, *embedded_id_b);
+    }
+  }
 }
 
-void BKE_lib_id_swap_full(Main *bmain, ID *id_a, ID *id_b)
+void BKE_lib_id_swap(
+    Main *bmain, ID *id_a, ID *id_b, const bool do_self_remap, const int self_remap_flags)
 {
-  id_swap(bmain, id_a, id_b, true);
+  id_swap(bmain, id_a, id_b, false, do_self_remap, NULL, NULL, self_remap_flags);
+}
+
+void BKE_lib_id_swap_full(
+    Main *bmain, ID *id_a, ID *id_b, const bool do_self_remap, const int self_remap_flags)
+{
+  id_swap(bmain, id_a, id_b, true, do_self_remap, NULL, NULL, self_remap_flags);
 }
 
 bool id_single_user(bContext *C, ID *id, PointerRNA *ptr, PropertyRNA *prop)
diff --git a/source/blender/blenkernel/intern/lib_override.cc b/source/blender/blenkernel/intern/lib_override.cc
index eec961d6dd6..1afe4d4d280 100644
--- a/source/blender/blenkernel/intern/lib_override.cc
+++ b/source/blender/blenkernel/intern/lib_override.cc
@@ -3784,7 +3784,7 @@ void BKE_lib_override_library_main_unused_cleanup(Main *bmain)
 
 static void lib_override_id_swap(Main *bmain, ID *id_local, ID *id_temp)
 {
-  BKE_lib_id_swap(bmain, id_local, id_temp);
+  BKE_lib_id_swap(bmain, id_local, id_temp, true, 0);
   /* We need to keep these tags from temp ID into orig one.
    * ID swap does not swap most of ID data itself. */
   id_local->tag |= (id_temp->tag & LIB_TAG_LIB_OVERRIDE_NEED_RESYNC);
diff --git a/source/blender/blenkernel/intern/paint.cc b/source/blender/blenkernel/intern/paint.cc
index 04784fe9378..b67696432d4 100644
--- a/source/blender/blenkernel/intern/paint.cc
+++ b/source/blender/blenkernel/intern/paint.cc
@@ -130,7 +130,7 @@ static void palette_undo_preserve(BlendLibReader * /*reader*/, ID *id_new, ID *i
   /* NOTE: We do not care about potential internal references to self here, Palette has none. */
   /* NOTE: We do not swap IDProperties, as dealing with potential ID pointers in those would be
    *       fairly delicate. */
-  BKE_lib_id_swap(nullptr, id_new, id_old);
+  BKE_lib_id_swap(nullptr, id_new, id_old, false, 0);
   std::swap(id_new->properties, id_old->properties);
 }
 
diff --git a/source/blender/blenloader/intern/readfile.cc b/source/blender/blenloader/intern/readfile.cc
index 1f1c5a48758..55d1bb29568 100644
--- a/source/blender/blenloader/intern/readfile.cc
+++ b/source/blender/blenloader/intern/readfile.cc
@@ -72,6 +72,7 @@
 #include "BKE_lib_id.h"
 #include "BKE_lib_override.h"
 #include "BKE_lib_query.h"
+#include "BKE_lib_remap.h"
 #include "BKE_main.h" /* for Main */
 #include "BKE_main_idmap.h"
 #include "BKE_material.h"
@@ -3095,10 +3096,17 @@ static void read_libblock_undo_restore_at_old_address(FileData *fd, Main *main,
   BLI_remlink(old_lb, id_old);
   BLI_remlink(new_lb, id);
 
-  /* We do not need any remapping from this call here, since no ID pointer is valid in the data
-   * currently (they are all pointing to old addresses, and need to go through `lib_link`
-   * process). So we can pass nullptr for the Main pointer parameter. */
-  BKE_lib_id_swap_full(nullptr, id, id_old);
+  /* We do need remapping of internal pointers to the ID itself here.
+   *
+   * Passing a NULL BMain means that not all potential runtime data (like collections' parent
+   * pointers etc.) will be up-to-date. However, this should not be a problem here, since these
+   * data are re-generated later in fileread process anyway.. */
+  BKE_lib_id_swap_full(nullptr,
+                       id,
+                       id_old,
+                       true,
+                       ID_REMAP_SKIP_NEVER_NULL_USAGE | ID_REMAP_SKIP_UPDATE_TAGGING |
+                           ID_REMAP_SKIP_USER_REFCOUNT);
 
   /* Special temporary usage of this pointer, necessary for the `undo_preserve` call after
    * lib-linking to restore some data that should never be affected by undo, e.g. the 3D cursor of