Yes, the auto-consolidation goes through all the photos in the project and checks each file. This takes a long time. (If you know exactly how the paths changed you can also change them directly in the database with a one-liner.)
It can happen that the changed path of the photo you consolidated manually if not meaningful enough to deduce how other paths changed, but this happens only in rare cases where the photos also changed relative to one another.
Could you share the old/new path of a photo you consolidated and the old/new path of a photo that Tropy did not fix automatically afterwards? This should help explain whether there is some issue involved which we’re not aware of yet.