Let me explain a little what I'm thinking so you can get an idea of what to look for.
crislapi wrote:1) Do you have expense reports for both checks (#1001 printed on #1002, and #1001 printed on #1001)?
The only way I was able to get MLS to print 2 checks with the same check number was to tell MLS the first check did not print correctly. This is a reasonable assumption to me: He printed #1001 on check #1002, noticed it after it printed, and said no. It would have printed fine except that the check numbers didn't match.
I could then close my expense screen, reopen it, enter a second check, print it as #1001 on #1001 as well, and this time say yes.
However, this approach only printed an expense report for the second check. The first one still sits there waiting to be reprinted. I can remove it by going to my view/update expenses screen. The "misprinted" check appears w/ ref # "not printed". If I open it, I can delete it, which removes the expense completely from MLS w/ no trace.
This leaves me with two checks printed as #1001, but only one remaining in MLS. I only have an expense report for just one of them, as well as an expense transmission confirmation report for just that one. If he can't find expense reports and/or transmission reports for both of them, this might be how the error occurred.
I'm not saying this is how it was done, but it's the only way I could duplicate it.
crislapi wrote:
2) Did one of the checks clear as 99991001 on your CUFS?
If the bank cashes a check before it has been transmitted, it will show up on your CUFS with the check number padded with 9's instead of 0's. If you do notice one of your #1001 checks with 9's in front of it, this would add credence to the scenario I mentioned above since it hinges on one of the checks not getting transmitted.
I would also look at the dates of the checks. Granted, when they were cashed is not directly related to when they were cut, but it might be useful info.
I'm also curious if they cut a check #1002 or if that one is skipped.