Talk with an HVAC company. There is a process for heating ductwork where something is misted under pressure into the ducts and it fills leaks. Obviously for efficiency but the process may work

You might get some collection of particles at the joints and the static pressure/noise may be a little greater but I doubt it will be significant. I'd just live with it.

You'll know not to use that installer again!

I think it's a safe bet you'll get accumulation of material at the joints which will create both additional friction loss and an elevated fire risk.

I don't understand why this question was posed to this forum of mostly homeowners rather than to the company who did the work.

"I don't understand why this question was posed to this forum of mostly homeowners rather than to the company who did the work."

Getting input from people helps to make better decisions.

Correcting this will be expensive for the contractor and me, will be a PITA and could damage in-floor radiant heat tubes or other stuff. I don't want to go through all of that if it's not necessary or recommended.

Many of the 'homeowners' on this forum are actually quite intelligent as are some of the 'professionals'.

It seems the purpose of these forums is to ask questions and get input. Perhaps I missed something about that.

To what extent performance suffers depends on how well joints fit. That is to say how far male edge protrudes into airstream. If joint design is similar to single wall wood stove pipe,there is no reason for concern. An indicator of well designed metal duct is a ridge and groove encircling pipe at end of crimp. Machining those require extra steps with more sophisticated equipment than that required to crimp male ends. I hope you follow that description.

Before doing major surgery to correct the issue, I suggest you do some performance testing of your dust collection system to assess how much of a problem it causes. If the air velocities are too low for the system to function reliably, that can be dealt with by purchasing a different blower/motor combination or a different motor for your existing blower--probably at a lower cost than the surgery.

After a period of testing, I think you'll be well served to do a visual inspection of the interior of the ductwork (a plumber with a fiber optic camera is a good option) to assess build up. If build up is a problem, you can perform periodic cleaning using the same type of brushes as a chimney sweep.