@Doitsu - sadly in this case it is the code at fault (and me to blame). In attempting to fix something else this week I broke the splitting where the hrefs are linked to the same page. Schoolboy error.
Edit: Ok, worked out the fix for our next build. Ironically it was an attempt to fix an old Sigil issue that Crutledge reported on the last thread which did the damage, of hrefs in the form "SomePage.html#" (trailing # but no fragment) not being recognised. Methinks the next Sigil beta build will be sooner rather than later once user_none finishes slapping me around...
To summarise - it is only Split which is broken with this build and only in one circumstance:
<a href="foo"> - No problem
<a href="foo#"> - No problem
<a href="foo#bar"> - No problem
<a href="#bar"> - If after split the #bar is on a new page, will not update href
As a workaround (such if you are importing a single HTML page to split it) just do a find replace to insert the name of that page before any links, so href="#bar" becomes href="../Text/foo.html#bar" where foo is your page name.