The game developer got it right this time. You CAN assemble and take apart any item you upgrade. So lets say you have upgraded a weapon to the hilt and now you find a better weapon and you want to downgrade the old weapon and upgrade the new.
This is simple go to one of the workbenches scattered throughout the game such as aboard the ebon hawk or the apartment when the game first starts and select the old item that has been upgraded. Now remove each mod from the old weapon and then select assemble. This will put your all of your mod supplies back into your inventory. Now bring up your new weapon and you can insert the mods you freed up and then select assemble.
Simple as pie.
This is awesome because now you don't have to hold onto mods like gold waiting for items late in the game. You can take advantage of mods as soon as you acquire them w/o worrying about losing them.