To comply with record retention requirements, a bank only needs to save a check in one format. If you are using an imaging system and saving the checks in a digital format, you do not need to hang on to the paper check. With that being said, it is a good idea to hang onto the checks for a short period of time. We hold ours for 90 days I believe. I think 60-90 days would be appropriate.
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Sometimes you have to burn a few bridges to keep the crazies from following you.