Huggy,
From everything you posted on here before, you run a very successful business and don't need any of us to tell you how to do it or how to charge.
That being said, I don't do service calls like this, but as long as you didn't lose money I think you did the right thing. Either they will appreciate that you gave them a break on something that wasn't your fault (hopefully leading to more work from them or their referrals). Or, they don't appreciate it and you know to never work for them again. Either way, tough situation and I think you did the right thing.
But I'm still pretty sure you didn't need anyone to tell you that.