Hating all those not-so-real ID types... Here there were two causes for the issue:
1) Linked shapekey ID was made local twice (once from mesh's make local, once by itself).
Solved by not explicitely making shapekeys (nor any other non-linkable datatype) local.
2) Key->from 'back pointer' to its owner was messing 'still in used' detection of linked data
after localization. Fixed with a hack for now, thinking correct solution might actually
be to not consider this pointer at all in libquery ID looper, since it's nothing like
and actual usage of mesh/lattice/curve.
Again, shapekeys as ID is a joke, those should be mere struct, they have absolutely nothing to do in Main, period. :(
Point 2) still demonstrates the need for better handling of IDs dependencies though,
so far we only hit corner cases, but think there could also be valid cases generating those
'dependency cycles' between IDs (ID a using ID b which uses ID a), this will have to be addressed some day...
cdc7a24d7b