Well, changing the frequency did not fix the problem, and when I played the sound files in audacity they were muffled, so it's as if they lost audio definition when they replaced files, but what did work was me going into the vanilla client playing the sounds while recording, and then exporting that recording as an ogg file. Thank you for suggesting changing the audio files themselves, I had not considered that. I suppose to avoid modding that actual client files you could have the game initialise the sounds from a different, new folder. Would it be against any rules if I recorded the ingame sounds in their best quality, and made a txt file to be executed from autoexec? Another question, would it be against any rules if I distributed those files with a disclaimer that I don't own the files?
Concerning the first question, I never did any recording ingame for that purpose nor have I actually done any recording, so I'm not sure.
As I mentioned before, some sounds in Sauerbraten have different (by that, I mean lower) frequencies, so obviously if they sound muffled in Audacity, that might be solely just how they were made. Not exactly high quality.
Now, distribution of those sounds? You'll have to look at the licenses for those sounds (there's a readme.txt located at the sound directory). On my honesty, though, you're just better off not redistributing those sounds since they're just modified vanilla sounds.
By the way, you haven't mentioned what particular sounds you were having issues with. What were the sounds you were having problems with?