Hi Ian,
Unfortunately, finding car body shops whose attention to detail is as good as you need is very difficult. How was the lettering applied? Did they spray the black base coat and then return it to you to apply the lettering? After that, did they lacquer the whole thing?
The base coat may be solvent or water based- depends on the bodyshop. The lacquer coat will be solvent based and as David says may well dissolve the letters.
As they have told you, rubbing down just the front will cause problems. I think to get a perfect finish, you would have to start again possibly using different materials. Not sure how you can salvage this.
Cheers
Nick