Hi Carol,
What versions of AP and BR is your client using? This matters as it affects what is possible when reversing checks.
If BankRec is used, that is always the place to do the reconciliation, and let the changes flow through to AP. It is most efficient to set BankRec banks to send reconciliation changes as pending statuses to AP (rather than None) to save time and prevent mistakes.
Make sure that the accounting is correctly defined in both AP and BR in regards to the GL accounts assigned on the respective bank codes for the bank and clearing account. When a check is reversed in both places, there should be a net zero change to the clearing account, and all accounting will be written to the respective reconciliation posting journals - so you can see what happened and if there are any differences.
Are both reversals happening for the same date? If not, then it is possible that different fiscal periods are being affected in GL.
Also look to see if they are reversing AP payments or cash invoices. There are options in regards to reversing cash invoices for AP vendors on file, so ensure everything is set the same way.
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Regards,
Softrak Tech Support