Re: Why did changing codec to Apple Pro Res change 25f editing timebase to 23.98

TBH, you'd be much better off converting all your material to ProRes before assembling it on a timeline. Yes, it takes time to do, but it'll save you time later, e.g., when you come to export. Putting GOP codec material on the timeline gives you the illusion that you're getting into the edit quicker, but it's a false economy in terms of the amount of time you will end up spending on the project by the time you finish.

I recently picked up a project which had 4 different codecs on the timeline and had every problem you describe, plus regular crashes. Converting the media to ProRes fixed it, which took time (a couple of days doing it in batches) and in the meantime, the FCP was much more stable with the sequence settings in ProRes even with source material in other codecs.