"As long as you do not change the cheque details like bank or Total amount columns you can change the posting without touching the reconcile."

Unfortunately, that is not true for US Payroll, because a Liability Check is a different transaction Type. You would use the Payroll Center function for Pay Liabilities, and you never use Write Check or Enter Bill.

So, first, it is very simple to ReReconcile. Don't worry about this part. You can change out "wrong" transactions for right transactions any time. Then, you Ignore the beginning balance and just reconcile to the same recent known ending balance, clearing only those transactions you affected, and you will get to a difference of 0.

You also can use a Clearing or Cash Bank, like this:

Get a report of everything they did that was wrong.

Use Pay Liabilities, for each cycle and Period and date and amount and check # that matches what they did incorrectly. Pay from the Clearing Bank or Cash Bank. On each Liability check, click on the Expenses tab and put their entry here as Negative, to the expense account where they created Double expenses. Hit Recalc. This must end at 0. "Parallel" and offset their errors like this, until everything is paid correctly.