Once you convert a book with calibre to a .mobi file, it will generate a TOC which is
required by Kindle. The generated TOC will appear at the
end of the document. The generated TOC then becomes a part of the document itself so if you try to use that new .mobi file as the input to use for converting to another format, i.e.: Epub, you are going to get duplications of the TOC in the process. If you wish to avoid this, use the original, unconverted CHM document to create an Epub or whatever other format you desire.
There is some confusion in what you say. First you state you want a .mobi document to read on your Kindle (which, again, requires that a TOC be generated) and then you talk about converting that to an Epub or other format. Why do you need another format?
For more information on this subject, you can refer to the calibre User Manual. Specifically, this link:
http://manual.calibre-ebook.com/faq.html . Look under the heading "What's the deal with Table of Contents in MOBI files?".
If this doesn't help, ask for more assistance.