Former ADA plea bargained a state jail felony for 3 years TDCJID probated for 3. Somehow the Judge also missed it and signed off on the judgment.

Error not caught until after MTR filed.

Can we reform the judgement and then file a new MTR or do we need get the Judge to dismiss the entire case and start over since we are within limitations or what? If we were to start over could we enhance which was not done last time?

Sounds like ineffective assistance for a lawyer to plead his client beyond the punishment range.

Defense will probably want to file a writ (as JB points out, on grounds of IAC). On adding the enhancement, you might want to take a look at cases on prosecutorial vindictiveness. If the failure to allege it before was simply an oversight you should be fine, but should your actions be perceived as retaliation (chilling a defendant's right to seek relief) everything could unwrap.