Even if the record has been removed, the duplication would only exist at Church headquarters (in the CMIS system). MLS will have no idea if there is a record being restored -- MLS simply submits the record and gets a new membership record number (MRN) back. I think you can safely assume that if CHQ cares about a duplicate, they will detect the situation and reactivate that MRN. Either way, you won't know -- you'll just get a MRN back. So I don't think you need to worry about it -- just work through the normal process.
Questions that can benefit the larger community should be asked in a public forum, not a private message.