My skimmer has a plug in the cup so I do let it drain back into the sump. I will do a few more wc, change carbon and then let skimmer run.

Draining it back into the sump won't do anything. You need to remove the water that overflows. That's where the highest concentration of chemiclean is

Yes! What he said.

Also you can feed a healthy dose of mysis right before you power your skimmer back up. It will kill all the bubbles for a bit then they will return gradually.