Experts and BHG readers answer.
how to re-position wall ducts to floor ducts
I'm not sure if you're referring to return air ducts or supply but I'll assume you're talking about supply ducts. You should just seal the ducts you are going to shorten. Use 3mil plastic to keep out dust and plywood to keep the plastic from being damaged. You also might want to change your air filter more frequently since the added construction dust will clog the filter quicker and you don't want to damage your unit.