We have a special tool we use to remove the coverglass, but unless you have access to a completely dust-free environment you can work in, I wouldn't recommend removing it yourself, at least not without taking a few steps first.
If you send a flat as a raw FITS file to
support@atik-cameras.com along with details about your optical train, we'll take a look and see what the best course of action is - it's usually possible to tell where the dust is from its appearance, so being sure it's somewhere behind the glass and not somewhere else will be the first step.
Jo