Deep Bite: Can Not Chew with Braces on?

It sounds like your doctor could solve the problem by adding a bite plate to his//her treatment plan.  A deep bite and correction with braces can present a challenge to the orthodontist.  An analysis of the deep bite will tell if it was caused by the upper front teeth come in excessively, in which case they would need to be pushed upward to correct the overbite (reducing a gummy smile) before correcting the lower teeth.  However if the problem is an over closed bite (no gummy smile exists) the problem is usually corrected with a bite plate on the roof of the mouth which opens the bite and would allow the lower braces to be placed at the start of treatment.  It could also be a combination of the two cases, which usually results in the use of the bite plate to begin treatment.  

This is a common problem in deep bite cases.  There are several ways to deal with this problem, including bite plates, platforms on the back side of the upper front teeth, or platforms on the biting surface of the lower molars.  In some cases, it may be easier to first place the upper braces and get the upper teeth into a better position so the lower braces can then be placed without having them hit the upper teeth.  Doing this sequential approach will not usually double the time for the overall treatment, but may increase it perhaps 4 to 6 months.