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I've also merged, split and renamed files pretty often in the Calibre editor, and I run the Modify plugin on all books I load on my Kobos, but with all options unticked, except for additional css. Haven't noticed any issues. I read kepubs on the Sage, but with header and footer always off, so I have no idea what they would display. The TOC usually behaves correctly. The only instances it doesn't are some self-pubs where I haven't bothered to fix the TOC in Calibre.
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