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I'm not sure why this is happening.
I tried dragging one onto the other, but that didn't work at all. I started deleting one of each pair, but after I thought I was done, I couldn't get the balance to match the last reconciled balance. I had to revert to a previous backup and redo all the work I had just done.
At a guess, the second "Pay Now" either caused the process of the first to act improperly, or couldn't itself process correctly while the first was still taking place. Perhaps, both were downloading a transaction list from the bank at almost the same time? In any event, it's a pretty serious error!
I already restored from a backup and have apparently fully recovered. As a result, thpugh, I lost the file containing the duplicated transactions.