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I've been converting all to EPUB 3 for a while. Could it be that? At far as I can remember, for years, any TOC entry that is merely the file like xhtml without an ID, selecting it in iOS in the TOC brings up the cover. I also always set cover to linear no if that makes a difference.
As for as splitting files and having the TOC entry change, also for EPUB 3, let's say all body tags have the same id, e.g. id="body". If I have something like Notes = notes.xhtml#body, after splitting it, the TOC entry changes to the last split.
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