When you save user tools, the dialog should default to the name of the user tools file you last loaded, which it doesn't. If you choose to save the tools under that same filename, there shouldn't be a warning that you're about to overwrite a file, which there is. Found in release 241.

It looks like the code does not really keep track of what was the last loaded tools file. This would rather be an enhancement then a bug.
BTW there is a warning displayed if you try to overwrite the existing tools file.
Thanks,
PN