I strongly doubt the cyclone would have any negative side effects as long as you have installed the correct size one for the application.
They have been used for decades in Ag and mining sectors, and are very effective.
The only negatives are when air throughput requirements are too high for the size unit, they will create restriction, and even noise pollution!
So long as you aren't getting these issues, I wouldn't worry, you could put a vacuum sensing switch on the intake to check.
Edit: how many horsepower is the engine?
Cheers


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