I admit that I do not understand the problem.
If styles are written in each head section of the xhtml file between the
tags, then after all, replacing this in all files with:
Code:
<link href="../Styles/Style0001.css" type="text/css" rel="stylesheet"/>
takes just a moment.
In addition, if you put your own css file in the Sigil configuration folder with the name
user-template2.css (for EPUB2) or
user-template3.css (for EPUB3) respectively, and when selecting the "Add Blank Stylesheet" command, you immediately have a ready-made stylesheet file.
Perhaps your problem is more complicated, but in that case show an example.
Edit: With a few EPUB files I think the whole job would take two minutes.