For certain reasons unrelated to this HOWTO I deleted the Basilisk's settings folder as guest via
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rm -r ~/.basilisk-dev/
Thanks to the helpful folks in the original thread in Intermediate/Advanced User Questions (link to that thread at the very bottom) I recalled the reason:
The way a live system works, and because all modules are read-only, there a special white out files that act as "this file or folder (and all sub-folders and sub-files of that very folder) should be hidden because the user deleted that file or folder" technique.
You can manually re-create that file or folder, but any such files from a later loaded module that sit in or "below" that folder path would still not appear in your life system, only the manually re-created file or folder would appear.
With "below" I mean this:
In my case, I deleted as guest ~/.basilisk-dev/ meaning the deleted folder was
/home/guest/.basilisk-dev/
and all and any files and folders "below" /home/guest/.basilisk-dev/ that are part of later activated module would still not appear in your life system:
e.g.
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/home/guest/.basilisk-dev/basilisk/
/home/guest/.basilisk-dev/basilisk/RaNdOm123.default/
/home/guest/.basilisk-dev/basilisk/profiles.ini
You have to find the one singular responsible .wh* file and only delete that one singular .wh* file.
The location is always to be found in /mnt/live/memory/ but the precise path could be different, depending on if you use the changes cheat code - or not. I do not use the changes cheat code and in my case this command gave the the file responsible:
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find /mnt/live/memory/changes/home -name ".wh.*"
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find /mnt/live/memory/images/changes/home -name ".wh.*"
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/mnt/live/memory/changes/home/guest/.basilisk-dev/.wh..wh..opq
There have been more hits for that search via the above find command, but I only deleted that one singular /mnt/live/memory/changes/home/guest/.basilisk-dev/.wh..wh..opq white out file to fix the issue and left all other white out files be.
Please take special care to not delete all .wh* files in your life system, only delete a single one when you encounter a similar issue as described here.
The original thread with some more background info can be found here: Module activation - folder doesn't appear in live system