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Thanks for the replies. Converting from the EPUB to MOBI does not fix all of the formatting issues. I also used the Kindle Preview application that was recommended, and I noticed that the hyperlinks that I made for the TOC in my HTML document were no longer active in the Kindle Preview app. Is this because I'm not using metadata/logical TOC?
If this issue is related to not having metadata TOC, is there a program which will automatically convert the hyperlinks in the "Table of Contents" section of my HTML document to a logical TOC in MOBI?
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