Duplicate entries entered as reconciled. Reconciles entered in register automatically.

This has been discussed on the forums but my experience expands on what others have said.
A fixed an account with multiple duplicate transactions. Had to go back and un reconcile and rereconcile. Once it was clean, I performed Update Now. The register was changed without asking. Went back in time and found the rogue duplicate and deleted it. Performed Update Now and the register was changed automatically. This time the matched entry as the one deleted was itself deleted without asking.

This appears related to the date and posting date being way off as is the update matched to the wrong entry. It is as if the 2 entries are somehow tied together.

I have seen entries not show up in reconcile until I entered one manually at which time both showed up in reconcile.

It is difficult to believe this can be fixed simply by adding or deleting as things get added/deleted automatically in Update Now.

My current recourse is to enter $0 "reconcile comments" which state the register balance observed for a particular date with the date the date that the register balance was observed. I use this info to go back and find when/where things went awry.

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