K2,
I encountered a similar situation when I switched from the ill-fated Cone
archival color inks to the MIS VM inks. The tubing was permanently stained
with the various colors, but didn't present any sort of problem when I
loaded the VM inks.
I recently needed to replace the carts again and as a precaution installed a
new support arm and tubing. When I removed the old tubing, I immediately
flushed the tubing with water. It still has the color staining from the
original inks and shows no signs of clogging from the VM inks. It's in great
shape still and ready to use again.
Tom Keesling
Intelligent Design, Inc.