If you put the check or invoice (or both) on the wrong customer, it can be fixed. Just follow these instructions:
Case: Invoice on Right Customer, Check on Wrong Customer
1. Use the "Returned Check Entry" to remove the check from the wrong customer
2. Enter the check for the right customer and apply it
Case: Invoice on Wrong Customer, Check on Right Customer
1. First, use manual invoice/credit entry to enter the invoice for the correct customer
2. Apply the check to it. Now the "right" customer's records are OK
3. Enter a credit for the "wrong" customer; exactly match the original invoice entry, including
dates, ledger numbers, etc. Just make all the amounts minus instead of plus.
4. Now enter a ZERO check for the "wrong" customer. Apply it to the two open items (invoice and
credit). There will be NO net effect on customer account or the general ledger.
Note: Any problem you have that you think is more complicated than this is really just a combination of the two cases. Solve it one piece at a time using the two cases above as a guide.