No Sigil does *not* "automatically removes the ../Text/I-1.xhtml part from the href".
Period. Mend will not do that. Nothing in Sigil will do that based on a simple save and reload. I have just tried it repeatedly.
So you are either using a really old or modified version of Sigil or some other tool you are using is removing that text. Sigil does not auto update links unless you use move or rename.
Assuming your code looks like the following:
Code:
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:epub="http://www.idpf.org/2007/ops">
<head>
<title></title>
</head>
<body>
<p>*</p>
<p>some text <a id="fn-021-bk" href="#fn-021"><sup>[1]</sup></a></p>
<p>more text <a id="fn-022-bk" href="#fn-022"><sup>[2]</sup></a></p>
<p>even more text <a id="fn-023-bk" href="#fn-023"><sup>[3]</sup></a></p>
<p><a id="fn-021" href="#fn-021-bk"><sup>[1]</sup> footnote 1</a></p>
<p><a id="fn-022" href="#fn-021-bk"><sup>[2]</sup> footnote 2</a></p>
<p><a id="fn-023" href="#fn-021-bk"><sup>[3]</sup> footnote 3</a></p>
</body>
</html>
The easiest way to achieve what you want is:
1. insert Sigil SplitMarkers immediately before the footnotes section in all of your files and then split all on Sigil split markers.
2. Then manually drag and drop just the footnotes files that were split off back down to the bottom of BookBrowser (keeping their relative order)
3. Then selecting just those footnotes files, Merge them to create your EndNotes.xhtml file.
The act of Sigil's merge will take care of making ids unique and keeping all links going to where they should go.
I have attached a test epub here for you to play around with.
I have already inserted the Sigil split marker (but you could do that using find and replace for something just before the start of the footnotes or manually using the Insert->Split Marker menu item
So give things a try to prove to yourself it all works.