Merging movies leads to loss of play history

It depends which version is selected first. When you merge, the item which is selected last will change its identity and therefore its playback history to the one which got selected first.
So if you selected your new version first, then the old item lost its playback history.

General rule: If you have converted your movie library (“upgrade matching”), you need to perform “Refresh Metadata” before you do a quality upgrade.
This “matching upgrade” is not complete without a refresh of metadata. Until you do it, all the items are in a weird state where they still have the guid of the old “Legacy” agent.
But if you add a new file to the library, it will get its guid from the new agent, which will be different from the legacy guid.

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