I agree, the core database records should only reflect the actual physical (or virtual) cards that exist, as accurately as possible.
Maybe the notes feature could be expanded (if it doesn't already have this) to have a functionality that lives with the card outside of a particular deck, so for example you could add a note "#zombie" to a token to indicate which side is sleeved on a double sided token, but you could also add wear notes or other notes that would carry with the card and appear in inventory and deck lists. I prefer this to dedicated double sided token functionality since it has a desirable general use case as well.
I'm suggesting this because the main issues people want to solve are:
1. How people sleeve their cards (tracked in notes)
2. How to avoid confusion where there could be two database entries for the same card (remove single sided entries for double sided cards)
I also recommend immediately changing the card numbering for all existing cases where both double and single sided database entries exist for the same cards, to head off future confusion about numbering once non-existent database entries are removed.
Based on this, a message should be sent to any members who have recorded one sided tokens that they will need to update to the two sided tokens, and ideally a list of their one sided tokens should be provided for reference in case they don't fix the issue before one sided tokens are removed.