It was my understanding disassembling the entire bolt carrier to get the firing pin out will wear out the assembly if done every time. Can i flush the entire bolt in hot water then follow with break cleaner or will water get trapped inside?
You won't wear out an SKS to the point of it even making a difference in the function or performance of the firearm as is.
It sounds like you left water in the bolt carrier aftercleaning.
Mix up some Ed's Red, it's dirt cheap and lasts a long long time.
Strip the rifle down, soak the bolt complete, gas piston etc in a pot of water, wipe it all down with a brush and wipe dry.
Spray water down the barrel, run a brush, one more hit of water, wet a rag with water and wipe down the inside of the receiver, rails etc
Then dump the water. Put Eds Red in the pot, dump the bolt the piston and all small parts you had in the water into the pot, it will displace all the water, lubricate, clean everything.
Spray some eds Red down the bore to displace all the water. Wipe down the inside of the receiver with a rag with some eds red on it.
Then you just wipe all parts dry with a rag, reassemble and pour the eds red back in the can for next time.
That's how I clean all my soviet guns which I fire corrosive in. Been doing it that way for many years, many rounds fired and never had a spot of rust. It literally takes 5-10 minutes to do it this way. Just wear gloves and make sure you run a fan or something when the Eds Red is out, it smells a bit and like any solvent you dont want to be huffing it in for any long period of time.