I did the same thing on one of my 540s, which after I drilled out of the basket inside the muffler and opened up the outlet, felt like it was starving on the intake side. So, I cut a 1/4" x 3" slot on the back of the cover, with a heated razor knife, and champhered the edges with a file. The slot goes from flywheel side to just across the handle. I kept the clutch side closed.
Comparing two saws (one factory-quiet one with modded muffler and cover-hungry), I haven't noticed any more filter clogging. If I flatten the chain on something, dust will get into the carb box just the same. With a sharp chain, it's almost easier to clean the filter on the modded cover, a few chunky Chips in there keep down the dust. hahahaha
IMHO, the modded muffler definitely likes the easier breathing at the carb end. On acceleration, the sound on the carb suction is almost as loud as the muffler, but different.