Just found a possible bug.
If you export a folder structure with links and linked objects in it - export and re-import mixes up the location of links and objects.
Affected so far: AE 11.2.5, 11.2.2 (not sure which components are responsible)
reproduction:
Folder with one subfolder in it,
in FOLDER are Object A and Link to object B
in SUBFOLDER object B and link to object A is located.
If you export FOLDER and re-import it (keep folder links), both objects A and B are in FOLDER and both links are in SUBFOLDER
Opened Support Ticket: PRB00136115