I use CLR on my Cerakoted barrels and there is no issue. Just don't let it sit much more than 15 mins and you will be fine. Follow CLR up with Kroll or something like it to make sure you get it out of the bore. It cuts carbon very well, however if you neglect cleaning you will have to scrub with it for a while. I use a copper brush and CLR for tough carbon buildup, may take several sessions but it has always come clean.Have you tried it on cerakoted barrels?
I only use it on stubborn carbon rings on the throat area.