Suddenly, Our check numbers look like the numbering increased by a good number of digits.

Checks are sequentially numbered. Someone typed in a dramatically higher number in the check number then saved. The next check is then sequential from there. Do yourself a saved search and look back to the first transaction with the new numbering. That will identify where it happened. You will need to manually (or CSV) all those transactions to get your numbering back

most likely cause of this is someone entering a confirmation/transaction number for an ACH