last year I had several times this issue with one of my Mimaki JV33's last Feb/March. we replaced almost everything we could except the ink lines. it started with one color and then others dropped out and I couldn't recover them no mater what new part was in the machine.
we eventually decided to change the print head after ruling out other cheaper part replacements. it helped for a few months then a similar thing happened again in sept.
my technician found out that when we replaced the print head in september, that the channels of the head were breached so whatever happened during all of our trouble shooting leading up to the print head replacement, damaged the print head so we wouldnt be able to save it even if we could.
we never did figure out the root cause of the problem.
This year we ended up replacing that printer entirely with a new JV300-plus.
good luck