Musescore deleted my entire score

1. MuseScore never deletes scores. Only you can do that, by a deliberate action.
2. Reopening old saved files (perhaps in MS3 format) in MS4 means that the next Save or Save as will change the score into MS4 format. And MS3 cannot open a score in MS4 format.
3. Always keep MS3 scores in a folder for MS3 format, and MS4 scores in a different folder for MS4 format.

You can check both in MS3 and in MS4 where your scores are saved by default:
Edit > Preferences > General > Folders > Scores