What are people doing to protect the barrel,s bore during the process ? 
I've never used anything to protect the bore during rust blue or brown.
Express or Cold rust, doesn't matter.
Wipe it out dry to start. No oil in the bore as with any other surface on the part.
No rusting soln in the bore of course..
Never had the bore or chambers damaged.
I usually run a clean dry patch through the bore after the bbl comes out of the boiling water tank and has dried off of it's own heat. Just to make sure there's no droplets in the bore.
When doing Damascus finish I do coat the bores with plain old shellac.
A heavy coating with a cleaning rod w/a rag on the slotted tip.
Several passes, let it set up,,then more again to make sure it's covered.
Clean off the muzzle and breech of any run over from the application.
The Damascus finish requires the bbls go into an etch dip and you have to protect the bore from that.
The Shellac holds up perfectly in the boiling water tank even with the many, many cycles needed for Dmascus finish.
Just to be on the safe side I admit to recoating the bores over the orig stuff at about cycle 8 or 9 just to be safe.
It can take 15 or so cycles for some Damascus finish projects.
I didn't always do the recoating, but something told me it might be a wise thing to do!
That Ferric Chloride etch works extremely fast even at the weak % I use it.
....So if you wanted to protect the bore with something easy to use just to be on the safe side,,a heavy coating of shellac will do it.
Remove it afterwards with lacq thinner, alcohol or even ammonia cleaner.
You'll be surprised how tough it is to get out of there. But it will disolve and leave the bore clean with some elbow work.
