The Florida law specifies the Florida Building Code as the building requirement. The builder does not need to issue you a letter of compiance, he just needs to do the repair. This isssue does not void your contract.
Under Florida law the building department does not share the liability. It is the builders responsibility. Request to see the engineering repair plan, check it against the as-built conditions. If you dont have the expertience to do the inspection higher an engineer, consider having the building official there. If the builder refuses, then legal councel should be obtained.
This type of repair is common, plumbers are know to be wood butchers. Typically I have just added a member(s) (2-2x12 or doubled the joist) on the side (s) on the repair area extending from 4 ft on each side to the full length depending on the repair.
****Warning****
Dont pi-- off the building department, you want them on your side. Ask the building inspector for help and advice, they love it! Consider not the alienating builder, this is not a big deal. Be friendly but firm, state the Florida requirements (engineered repair) and your expectations (repair made to a engineered repair plan) and thats all, try to keep emotions out.
Hope thats helpfull
Cheers
Boo1