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I'll look into autonumbering duplicates. Thanks!
Edit: Fixed. Copypasted metasprite labels will append a unique number ("_1" for example) instead of "_copy" in future versions.
I'll look into storing it in the config. Thanks for bringing it to my attention!
It seems to already be in it. You need to go to Preferences (ctrl+p), pick the Export tab, select "ask metasprite name" checkbox, and click "apply and save".