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@Starson17: like theducks, welcome back. I hope the future is rosier than the recent past seems to have been!
Re merging: I haven't touched that part of calibre. I never use it so I can't even describe what it does. I do know that db.set_metadata will update custom columns from a metadata object, but I have no idea if abd when it is called. I can imagine merging working one of three ways: the existing record has the master metadata, the new record has the master metadata, or fields in the new record that are not in the existing record are added. The last one isn't exactly easy to do.
You seem to be saying that you want the new record to be the master. I don't see that as an option, but it should be possible to do. You would call set_metadata on the existing record, giving it the mi from the new one, possibly setting force_changes=True
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