In testing I’ve also encountered this issue. For some reason it deletes the pre-existing app-x.x.x folder in place of it’s own. I guess someone on the Citra team decided it was okey to do this now that the location changed 5 months back.
I don’t think you can recover the files anywhere from Windows, but they should be recoverable by a 3rd party data recovery program. In fact, I know they are as that’s what I just did (while writing this). Their’s plenty online, pick and choose your favorite by doing a little Google-fu. I ended up using EaseUS Data Recovery and it found the folder during a “Deep Scan”. All the files inside the folder was recovered fully too which is great.
When you’re done recovering the files make sure you move them to the new location by following the guide Hexagon12 linked to above. Happy gaming