I was looking at ways to add an "All CSS Files" option to our F&R parameters, but my head very quickly spun when trying to grasp the logic of that code.
The only way to currently do regex processing on css files is one file at a time with "Current File" selected. I think many would like an "All CSS Files option." But from what I saw, it looked like adding that option would require a minor overhaul of the existing F&R codebase.
But even that's not going to help the OP "batch process" css from many individual epubs. Sigil is really not geared toward batch processing
at all.