With my calipers, I basically cut the old flexi in half, the top bit, I've plugged in so brake fluid not leaking anywhere, the bottom part of the flexi, with the caliper, I've submerged fully in bucket of hot water with Deox-C fairy dust/citric acid, with just the cut off flexi sticking out. The caliper has seals that prevents any water getting inside the caliper if you don't plan to refurbish it fully it can stay like this in the bucket until its fully derusted. Afterwards, you just rinse it in water and paint if you want, with whatever paint you have. I suppose, you could even just submerge even the bit where the bleed nipple is.
Refurbing it fully, means at the end of this process, you just pull out the piston completely, swap the rubber seal and boot and piston if you want/need to, depends on how far you want to go really here. Its all easy work, just extra costs and time. New pistons are a tenner on eBay, rubbers are ~£20 for a pair.
1997, 4.0 LWB X300 - Unlucky car but still a daily driver.
1988, 3.6S XJS - Never ending restoration project.
1994, 3.2S X300 - Accident damaged, October 2015. Gone!
1994, 3.2S XJ40 - Long gone.