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The only chapter editor I've seen is in Handbrake (I haven't looked deep into the subject, though). Unfortunately if that's all you used Handbrake for you'd have to demux the chapters file out and remux it into your "master" video render.
Sounds annoying to do, but if there's no other way you find, at least it should give the results you want. Just not conveniently.
Edit: I do think some NLEs let you add flags or markers in the timeline and during export you can choose to set those as chapter points, but again, haven't looked into it deeply.