if the inline TOC exists as a separate .xhtml file (say, TOC.xhtml), and all you want to do is change the position of the TOC in the book (say, from the end to just after the copyright page) in Sigil all you have to do is drag the TOC file (in book view) to the position you want it to be.
This feature may be munged up in version 0.4.0-RC1, however. And it won't work for any version if you're running under linux with the KDE desktop environment. (Not without some hacking of the sigil.sh startup file, anyway.)
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