I haven't figured out how to do this, if there even is a way that is.
Every now and then I'll go through my entire craft bag and pick out items that I want to sell. It's not exactly a quick process.
So after spending a while handpicking all my items, I go to my bank and find that the guild stores a bugged - no listings available, won't let you list new items etc
Quick fix - log in and out.
BUT then every single item I have picked out of my craft bag will be chucked back into it whether I wanted it to be or not. So I have to go and fetch them all again.
This is a very specific situation I'm aware, but frustrating nonetheless. I would love there to be an option to keep materials from being deposited back in the craft bag.