Hello,
I don't know where the text files that you attached are coming from, but they don't look like any backup that Adagio does either from the File | Backup menu choice or from a DataCare backup. You need to check the documentation you have on the backup you are creating. It looks like the backup is just replacing files (since it shows some being deleted before their replacements are added). This is a bad idea. Adagio backups should be new ZIP's of the whole set of data files.
Nothing in the conversion should delete any orders or lines from orders. Your Adagio consultant may be able to "stitch in" the historical orders if they are important to you, but it is not a simple process.
Also, there was a recent Service Pack to OrderEntry 9.3A (181214). Please confirm that this is the version we are talking about.
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Andrew Bates