I think basically what happens is Mac A says “here are indexed documents in /FolderA/”, and tells Mac B “hey, there are indexed documents at the following path: /FolderA/”. Mac B (on which the files are located in FolderB) says “hey, they’ve gone, the user must have deleted them; hey Mac A, you can get rid of them”. So Mac A deletes them, and at the same time - because FolderA is synced to Dropbox - deletes them from Dropbox.
This happens because indexed files are expected to be present at the same location (path) on all Macs.