Have /resourcemarker retag (and incidentally delete), only delete tags that match the style of potential automatic tags. something like only deleting tag that use an ore icon and start with the ore name.

This way, manually placed tag wouldnt get deleted alongside the automatic ones.

Yes, please. My suggestion would be to tag the labels with the prefix [RMM] and then only manage labels with that tag.

I have a ticket to address this issue. Adding more notes about the issue there.

Thank you for reporting the issue. 🧡