There was a new feature introduced in the fix for
MNT-14362: Document selection is now maintained when the user navigates around the document library.
One of the problems with this is that if a user selects a file in one place, then doesn't unselect it before navigating elsewhere that file remains selected and will be added to any other items the user selects. There is potential for data loss here if the user performs a multi-select delete after navigating and doesn't check the list of files carefully.
I think the code (in r111482) has introduced multiple bugs, including
ACE-4702 and MNT-13640 and should be reverted. Other options could be explored to fix the customer's original requirement, like multi-select on search results (so they could search for all the files they want to modify and then select them all).
If that feature is required, my suggestion is that it should probably be added to a development backlog, validated and properly thought out before being re-implemented.