So, you want to run refrigerant through piping previously used for glycol? Yikes !!
If I were to be doing that, I'd flush the lines with copious amounts of water first. Then I'd schedule a tanker full of R-11 so I could flush the lines real good with that. Then as a final step, I'd plan on changing the compressor(s) oil a few times, just in case.
I wouldn't plan on the filters catching much. The idea is you don't want anything left in the piping for the filters to catch.
Good luck