This happened to me too, independently on two Macs with different Photos libraries. It's a very strange bug where after a library migration Photos.app will delete some pictures and videos from the Masters folder inside the library. The deleted files still show in the UI because the app uses seperate thumbnails for that. But the original files are gone. I only noticed it because some videos where not playing anymore and also exports of the files did not work.

I tried to narrow down what went wrong. Launching a previous state of the library on Mojave from a backup deleted the same files with the following output in Console:

Photos Import failed during master recovery for path: 2018/10/08/20181008-093231/28f7a73f-1737-4pb6-9275-1c35dwb8a30a.JPG, Error Domain=com.apple.photos.reddwarf.ingest Code=1 "Removed version uuid: Gvj78Pses+eRzULLoWJ83g because imported master was either removed, or chosen as the candidate master during de-dup" UserInfo={NSLocalizedDescription=Removed version uuid: Gvj78Pses+eRzULLoWJ83g because imported master was either removed, or chosen as the candidate master during de-dup}

Try this (after doing a full backup of your wife's ~/Library folder):

Option-Command-O on the /Applications/Photos.app. It'll go into repair library mode and might fix things.

Yeah, tried that already, no dice. :(

I saw this happen with me as well. For some reason Photos somehow completely lost track a couple years of recent pictures. No idea what happened here.