Thank goodness you have this little one now. Even though he is hiding, he is also learning that the horrible things that were done to him before are not happening now. He may be frightened but I think it will get better over time. You are an angel to have patience and love to give your little Beans. I liked the suggestion to maybe just do one at a time and just take a tiny bit off at a time.
Now I have a "Bean" story to make you smile and take your mind off the worries. When I was on recruiting in a very rural area, I kept calling one young man who had sent in a card requesting information. His mother would say, "He is walking Beans." So, I would call back again, after getting told three times in a row that the young man was "walking beans" I had to comment, "He must really love that dog!" The lady laughed for a good 5 minutes before telling me that "walking beans" was something they did in the field. They walk through the rows of beans, cutting out all the stuff that is not supposed to be growing there. So, months later when the young man was leaving to go to bootcamp, he sort of grinned and said, "Hope someone will be walking Beans for me while I'm gone." They really got a kick out of my mistake.
Have fun walking your Beans!