If this was carried out by the vet I don't see why any damage should have taken place although perhaps the only damage would be of the psychological kind, lol.
I have an 11yo rough collie that required to have his anal glands squeezed and I proceeded to do it (and yes, I have done this before several times before to other dogs) and he has never forgotten. This was 8 years ago. Now I find that unless I have a brush in my hand, I would risk my hand being bitten as he seems to think that I am about to give his private area another squeeze. If I am armed with a brush then it's smooth sailing as he realises that I am only going to brush him.
You say that he is having trouble going to the toilet, what kind of trouble?
To avoid anal gland problems it's best to feed him foods that are going to harden his poo so every time he needs to "go" the poo gives his glands a good workout. Raw bones should work a treat.
I have always had BIG dogs and none of them have ever needed this process (anal expression) it seems to be a little dog thing. I just rescued a Little Terrier mix and he scoots every once in awhile. The anal expression stopped him from needing to do this.