As you have asked, this is a very non-openlp question. I have never used Prezi, but I have used the "Show Desktop" feature extensively over the years - for instance, here we never use the Powerpoint integration, instead we blank to desktop and use Powerpoint standalone. We use it also for playing videos (we have never got the embedded media player to work).
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So, I can't see Opelnp interfering with Prezi or any other program.