Since we started Adagio last year, whenever we do a Day End on OE there is a pop-up... "Document (a long list of order numbers in random) already exists in this history datafile. Do you wish to overwrite the existing document in history with this document?" We always press "no" to it. The list of random order numbers keeps getting longer as we keep putting new orders. Is there any harm if we press "yes" to overwrite them?

When you post an order and then run Day End, the order will be written to the Historical order data file. If you later on edit the order and make changes (such as adding another item, changing the salesperson, etc), then you are in a scenario where the order information is different than what exists in history. Upon running Day End, you would receive the message you are now getting.

Assuming that any changes you make to orders are valid - and why wouldn't they be - then there should be no harm in allowing Day End to overwrite the existing historical orders with the newly updated orders. It would be prudent to make a backup of your data (use the Related Data backup from the File / Backup menu) before running Day End and overwriting history.

If you don't choose to overwrite history, you will continue to get these messages until you do, or you purge the order from the Current file. In the latter case, the order information in history may not be the same as what the final order information was.