Hi Mavis,
With the errors you received before, the likely result was that information was missing. Doing a Rebuild will synch up existing data, but it cannot recreate missing data. So as you indicated, the end result would likely be that the data is fixed but some documents will be missing.
The fact that the numbers are missing is not a problem - they could be missing because they were manually deleted, or purged from History, etc. The data should be safe, but you should do a data backup before doing too much more work.
You'll also need to decide what to do with those orders and invoices that are missing. Re-enter them and ensure nothing else is double-posted? Or manually deal with these few, if everything else is correct in IC/AR/GL? That would be up to you, perhaps with some advice from your Adagio consultant.
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Regards,
Softrak Tech Support