Hi gbglatz,
You are correct that Adagio OE would have to be used to move the purged documents into the Adagio OE history files. If someone inadvertantly ran Day End from Accpac OE, everything still would be OK unless they chose to delete the documents 'older than X days' towards the end of the process. Should a user choose to purge, then those documents are irretrievable, short of restoring from a backup.
Adagio OE and IC will work simulataneously with Accpac Plus OE/IC 6.1B. As you have noted, there are some processes that will have to be adhered to (such as doing Day End in OE with Adagio) if you wish to write to the data files unique to Adagio.
Best of luck with the install! I'm sure everything should go just fine.
Regards,
Softrak Support