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Yes Sigil will not like that link to "#Tag" unless somewhere in the file a real destination for the link exists with an attribute id="Tag" in a case sensitive manner.
Sigil can not update already broken links. It needs to find that id attribute someplace and update it if it ends up inside a separate file.
So fix that first. If there is a real destination for that href, change the #Tag to properly point to it. If there is no destination for that link, remove the link to nowhere.
Once all your broken links are fixed, then Sigil will happily split this huge file into normal pieces at your inserted split markers.
But that Sigil feature requires good input (properly matched sources and destinations, else more links may get broken.
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