Does Crates modify or move my audio files?

Short answer: No — Crates will not touch your files – unless you ask it to. 

Crates will not take initiative to alter, rename, or move your music files without your permission.
If something seems to have changed, here are the most common explanations and fixes:

1. Crates, by default, does not write to your audio files.
   The only case where Crates writes anything is if you enable the setting “Write ID3 tags to file” (found under Settings > General).
   When enabled, Crates simply updates the metadata (artist, title, tags, etc.) inside the file — just like any other tag editor. This doesn’t alter the audio data or moves the file.
2. If another app (like Apple Music) can’t find your tracks, it’s probably because the file paths have changed somehow.
   For this to happen through Crates, you would need to perform an explicit action that moves or renames the files — for example, using “Rename”, “Move” or “Move to Collection” combo action 
   In that case, you can easily fix it by relinking or reimporting the files in your other app.