I found the problem when I arrived at Raxus Prime (the second time) I lost all the sounds for:
1. Blaster Fire.
2. DMM sounds (glass, metal, etc.)
3. Some destruction sounds (ATST landings, ASTSs being destroyed).
So far, I haven't found a fix for it. I'm in communication with Aspyr about another issue, so I'm going to ask them about this one.