Hi Mark,
Once you complete restoring your lost data to your QuickBooks (QB) file and sync with Method, the data that was lost in Method due to synching with the “bad” QB file will be restored in Method. Method will not remove your restored data from QB upon sync, as the request to remove this data originally came from QB. As a safety precaution, I recommend that you backup your QB file before doing this anyway, just in case.
When you synced with the “bad” file, it would have likely created several DeleteFromDesktop conflicts due to Method being unable to locate the data in QB. These may be resolved once you sync with the restored file, depending on how you restore the data. If the conflicts are not resolved, just verify that you are able to locate the missing data in Method and they should be safe to delete.
I hope this helps.
-Audisho