We've also seen this with our larger clients. I believe that anyone who we have had to set this up for has had gridview, so we have just created a view that matched the file there.
If they don't have gridview, could you create the file using the cheque reconciliation grid from Adagio, export to excel, and then use a macro or a batch file to add the details that you mention are not possible in Adagio?
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Lauren Stief
Stief Group
Adagio Solutions and Support
1-800-540-3164