If you compress them the usual rate music is compressed to MP3 then yes, you will lose some of the effectiveness. The Holosync soundtrack becomes redundant but the Paraliminals will still work if you have retained the stereo soundtrack. How much of the Holosync you lose depends on how they are compressed. If you save as a 256 bitrate you will retain higher fidelity but this bitrate is rejected by some CD players if you are intending to burn them onto one CD.
Then it also depends on which compression method you use VBR, CBR or AVR. VBR is the best choice for something that has an entrainment soundtrack.
When you convert to MP3 another factor to watch is the stereo soundtrack. You want to keep the left and right channels separate for true effectiveness of the Paraliminals.
How much you lose depends on how much you compress. Less is best.
Alex