Lee, yep by all means clean them, (The Filters), and don't be afraid, all this rubbish about not touching your filters, don't clean with this and don't do that.
I am proud to say i have an optical system that is always a spotless as possible, and have no dust or dirt issues.
I probably over do it, i admit that, but each imaging session i air blow the front and rear lenses of the system and also following the nights imaging, before the caps go on.
The filters can, and do get dust on them sometimes as well, and it is not a problem to take them out of the system, get a good quality cleaning cloth, something like you would clean your glasses with and go for it.
First blow the dust of as best you can, then just polish it between the fingers until it shines,

and put it back, the filter will survive,
I believe it is rubbish how people are so afraid to touch filters and clean them.
I have taken filters out of a 49mm frame and grinded some of the sides to fit a 48mm frame, polished it up, refitted it, and it is fine, with no visible
signs of damage.
I will shut up now and wait for the flack.
Leon