Yes, you will follow the same procedure you did for flushing by running the initial fill cycle again. To do this, your carts will have to read Full again, then only way to do this is to run the chips down to empty. What I suggest doing is, using the flushing cart chips for this, run regular cleaning cycles or purge images through QTR to empty individual channels. Once your chips are reading empty on your flush carts, swap them out with the Pigment carts (after refilling) and install into the printer, at which point they will read full again and you can run the initial fill.
OR you could purchase a new set of chips to install on your refilled pigment carts and start right away.