I'm not sure exactly what you're considering, but if you mean to delete all replicas of the databases and create brand new ones that therefore contain no deletion stubs, I wouldn't do that. The databases will also will have new replica IDs and new database IDs (a hidden value), so people who have the database in their bookmarks, their clients would be expecting a different replica ID at the old path. This is likely to cause problems, especially if they create a local replica.
I would suggest rather than deleting and recreating all the documents, you only delete documents corresponding to rows that are actually deleted, and only update or create documents for rows that have been actually updated.
Performance basics for developers (whitepaper)
briefly discusses this exact case. The sandbox download referenced in the article contains an agent showing how to replicate data with a relational database.