Keeping Metadata of Removed and Replacement Content

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You might be able to use the Trakt plugin to sync watch history. Dates are all you or you can utilize an external media manager that handles that for you (I shy away from dropping names, I have preferences but that's mainly due to my experiences and how my ecosystem is set up).

Database changes are not likely to happen. There's one on the horizon that has been in the works for a long while now to hopefully resolve a lot of gripes about legacy by stuff, but I'm not about progress. Check out the GitHub if you want to see the details.