Yes, the Generate UUID script doesn't currently change the matching uuid in the toc.ncx file. Mainly because I forgot about there BEING an id entry in the ncx!
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And when speaking about not knowing: at the moment Sigil monitors the tmp files and reacts immediately to any changes - is it reliable feature?
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It can be a bit flaky, actually. If you look at the bash scripts, you'll see some commented out lines I was experimenting with. If the Sigil UI doesn't seem to react to your changes to the tmp files (visually), you may have to experiment with those commented out commands and see if one works better than the other for you.
Launching a terminal (gnome-terminal in my case) from the bash script and executing the commands seems to have pretty reliable results, though. Seems Sigil likes the "editor" to actually take the focus away from it. It's not a problem on Windows since it always opens a terminal window when launching the scripts.
Something for the TODO list is to modify the Smarten Punctuation script so that if no punctuation is altered, it doesn't save the file. The way it works currently, the file is ALWAYS modified. It works for what
I want to do with it, but that may be sticking point for other users.