Is it you who changes the file name in the downloaded artifact folder of
HTTrack? If yes - out of curiosity - why would you do that?Keep all files
untouched in the folder and let HTTrack manage it. But I am eager to hear what
your use case is.

The explanation why it is "changed": 
it is most likely deleted, and re-downloaded via a subsequent HTTrack run. And
this looks to you as if the file gets "renamed", which indeed is not.
Why? Because your manually changed file does not match any file on the
website's server side so to say and by default it will be deleted. You can
lookup in the manual for the keyword "purge" and how this can be disabled.
However, without further details on why you need to change the filename it is
not possible to give a better advise.

A single changed CSS filename will be also of no value, as it won't be
recognized any other artifact, which linked to the original downloaded CSS
file.