Similar here on MacOSX 10.14.6
Possibly happens when attempting to update a file, because first efforts to save file do save as expected.
Also, Save As with a changed name does work if name change is sufficiently changed.
UPDATE-Today it seemed as if this was due to saving to another HD; and perhaps Mac/Mojave failed to regard my spare, internal disk as my designated disk for saving files... After further work on a folder with 35 new "afphoto" files, the "Save As" function was not reliable, (after a few more ,new save-attempts).
The ability to edit many photo files is important, so I wish I had not started this work collection, because, at this point Affinity does not save my most recent "afphoto" work! Perhaps a clue is evident for the developers here, that the problem allows some work arounds but finally stops saving work files of users, perhaps because too many afphoto files are open, but I have lots of RAM and disk space. Closing off some windows does seem to help.