It looks like "miraculously"  checks are now being marked as cleared again.  However you will still need to go and reconcile the bank account to mark older checks as cleared (ones that matched while the clearing function was "broken").  Remember you can do mid month reconciliation as needed or you don't even have to finish the reconciliation - just use that to clear checks.

What is frustrating is Quickbooks won't ever acknowledge this happened or there was an error.