With my CFC I'll run hot vinegar thru it if I haven't used it in a while. I use a funnel. Then flush it with hot water.
I tilt it on an axis to run all the water out.
Run sanitizer thru it (Idopher) A couple times or cap it once I have a solid stream with the funnel still full. Drain it with 15 min or so left in the boil, run the sanitizer out, then hook it up.
Let the hot wort flow thru a little before I turn the chilling water on.
No issues yet.