I have no idea why is this even happening. I've been trying to replace a bunch of sound effects and nothing happened up until today. (Said files are just minor gun sound effects, mind you.) I can't even log for some reason, I can't help but blame it on the Anti-cheat at this point.
I've been making modifications on sound effects and looks of planets, systems etc. and nothing happened. I believe there's no restrictions on them. Gun effects are a bit tricky however because they have to play very quickly and I believe they have to be in the correct format. Are you sure your gun sounds' format doesn't differ from the original one?
If nothing helps, seek out admin help. There is a dedicated thread for this on the forum.