From my experience, when you import payroll files it unfortunately bypasses any built-in checks or prompts about inactive employees. Thus, you can pay terminated employees, however if he was in the file generated from ADP then ADP must have processed a check for him. When you void that check in ADP it will create a void record that you can then import into Sage and all should be well. EDIT: I re-read the question and it occurred to me that you must not be using ADP to process the checks or else you wouldn't be importing that file into Payroll but rather into the GL (we briefly used ADP and imported the ADP generated GL transactions, but no payroll records as they were doing the taxes, W-2's etc.) So, my answer above is probably not relevant, sorry, my only suggestion is that you MAY be able to use a script to look at their status with PR_Employee_svc before processing, but I'm not able to give you any examples or advice beyond that. On a side note, we never not mark them as terminated but rather inactive in Sage or else you will lose all of their history when you close the year.
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