Since I have an Apple Music subscription I decided to enable Sync Library which primary does:

1. replace lower quality audio files with ones from Apple Music
2. for unmatched files, upload them to the cloud (not your iCloud account, max 200 MB file size)
3. make that music available on all your Apple devices

I made a backup beforehand. In the end, after checking a couple of months later, it did not delete any files.

It did move stuff around, especially for my use case where I set album artist so that say Hannah Montana is grouped with Miley Cyrus. For that though just opening file info in Apple Music fixed it so I'd recommend using list view to view all your music files then do get info on one and scroll through your whole music library.

The above should solve most problems. I noticed some albums got moved to Compilations because the Album is Compilation flag was enabled so turning the flag off fixed those albums.

That's pretty much it. Much less troublesome than I thought it'd be.