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I have H1 and H2 tages for everything and each of those has a tag like this <a href="images/index.html#ch1. Why would this be in the images directory instead of the text directory?
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I don't know why those hrefs would be like that, but that is the exact problem, right there.
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In any case I tried changing this to text/index.html but just got more errors when I tried the validation tool again.
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Everything is case sensitive. There is no 'text' folder in a Sigil-built ePub. There is a 'Text' folder. Change all the hrefs in your html ToC to:
href="../Text/index.html#ch1"
href="../Text/index.html#ch2"
etc...