You need to contact your Adagio consultant. He/she has a fix for this situation.
More detail: earlier versions of Adagio (and ACCPAC Plus), did not correctly set an internal flag on deleted batches, but "got away" with that because they also did not check for the correct setting. GL 9.0 does check.
The solution will be to install a "hot fix" from Softrak and then run the data integrity check which will correctly set the flag on the deleted batch(es).
The good news: this only occurs on the first year-end after upgrading to Ledger 9, and will not show up in the future because, of course, GL 9 correctly sets these indicators,
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Ralph Allan
Business Computer Centre
Prince George BC Canada