When you create a 'master' on a DP recorder, it isn't really any different than a bouncedown of a mix. When you go to burn the CD it is the pair of stereo tracks it uses. Ideally they're the final version it will be using when you burn to a CD. You can always trim it again and make another 'master' of the master, as really all it is doing is making a bounce recording of the stereo mix onto 2 tracks it will recognize as the 'master' when it is looking for what to put on the disc.
It would be less trouble though to just do all your trimming before you bounce it all to the master stereo L/R. When you 'master' on one of these kind of recordings, the idea is to make the last, end-of-the-line what you will hear on the CD version. If you are going to trim it afterwards, you can do that just the same as you would have done it before, but you will just have to re-bounce it again to get the new 'master'. It really doesn't make a difference except that its quicker to just do it once.
