Audacity lost data files when I saved project

I opened an old project and it offered me a recovered version where it must have crashed last time I accessed it (it’s been a while). The recovered version looked fine and played well so I pressed ‘save as’ and selected the original project aup. When it saved it lost 88 data files and part of the project disappeared.

I’ve spent the last hour searching for the files showing as missing in the log but they’re not appearing. My question is, the files must have been accessible for the recovered version to play them, so they must be around somewhere right? Where could they have gone so I can go fish them back out?