By blocking the exhaust you only run the risk of causing your bike to run rich, possibly fouling plugs and making carbon deposits. It won't blow anything up or destroy anything.
As a reference, I had a stock CBR f4 muffler adapted to my KZ's 4-1 header. The thing was pretty quiet, but didn't have any pickup. It would go, just not fast. When I popped it back off to get my performance back I just put the open megaphone (the other end of the extremes), it went way lean and I had to move my jets.
The catch is that the EX can oft times go from a stock exhaust to Sarachus (or about any exhaust) and not need anything more than a pilot adjustment. Personally, I think you could put your extra baffles on, go to the track, pop them back off, and never touch the carbs. Heading to a "local" track likely won't be a big deal with fouling and such.
Did you just buy the Sarachus for the track? I don't understand the reasoning in buying the pipes and just plugging them up. In the amount of time it would take to install and remove the noise killers you could add about 45 seconds and just swap the mufflers before you leave home. Maybe your area is different than mine - I don't think anyone here would care if I ran "loud pipes" once or twice a week when I was going to the track. Heck, I could slip the KZ in and out of the apartment complex I used to live in with nary a complaint. You just have to be ready to drive with the choke on and not touching the throttle any time you can avoid it

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