I have no idea and without pics at least how can we answer this at all. In my head flex ducting is not a good idea but I need to see the situation for sure. I think moving air moves better in a smooth duct .

I'm afraid that was a big mistake, going from hard pipe to flex duct. You should have just had the old ductwork insulated. Too late now. The ductwork is totally inadequate as you have described your situation. It needs to be fixed by the contactor ASAP. If they drag their heels, go to Home Depot and complain.

What sktn77a said!

Flex duct should NEVER be used (not for HVAC nor bath exhaust fans nor dryer vents nor for any normal duct in a house). It results in too high of static pressure which reduces airflow. Even a perfect installation of flex results in poor airflow.

Why were you having your ducts replaced?

I did a review of available products and chose to have a Fantech remote mount exhaust fan installed when replacing a bathroom exhaust system. It came with flex duct, as do other exhaust fans made by most manufacturers. Fantech even sells flex-duct.

I'll take the advice of a well regarded equipment manufacturer over that of someone who's not in the business. I agree about using hard metal ducting for forced air Heat/AC systems and clothes dryers but bathroom exhaust systems and fans are different.

Inevitably flex duct results in numerous low points in a Bath Exhaust Fan exhaust - warm moist air and low spots results in condensation and resulting problems.

In general, HVAC systems perform better when sheet metal ducts are used for main trunk lines and the use of flex duct is limited (flex duct produces higher friction loss than the same diameter of smooth duct.) A ban against the use of flex duct is a little severe. Indeed, it's useful for isolating equipment vibration and noise. The higher friction losses can be dealt with in the design phase and equipment sized accordingly.