Issue was nasty hidden one, the dual status (mix of local and linked) of proxies striking again. Here, remapping process was considering obdata pointer of proxies as indirect usage, hence clearing the 'LIB_TAG_EXTERN' of obdata pointer. That would make savetoblend code not store any 'lib placeholder' for obdata data-block, which was hence lost on next file read. Another (probably better) solution here would be to actually consider obdata of proxies are fully indirect usage, and simply reassign proxies from their linked object's obdata on file read... However, that change shall be safer for now, probably good for 2.79 too.