Painting disassembled or assembled?

The figure I'm currently working on I painted while disassembled. I heated it back up with a hair dryer because I didn't want to risk loosing paint when boiling. I use model master paints and had no problem with paint chipping when I reassembled it. I used no sealer, no super glue, nothing. I was actually surprised at how well it worked out because I painted without thinking about reassembly. I heated the female end (for a long time), if you heat the male end it won't pop in correctly and you will end up having to take it apart again.

Hope that helps.

I always paint certain parts whilst the figure is in pieces. I paint all the parts that do not need heating to reattach them, for example the ab joint, shoulder joints and neck sometimes I do the hip joints too depanding on the colour. I then glue shield all the parts I have painted before reassembling. I find this the best way to ensure all possible visible parts are painted and also invisible parts, pointless I know but that's just my technique. For joints that need heating to take apart and put together, I usually give them a rough coat whilst still assembled then move the joint thoroughly to see where the paint is chipping then take them apart sand down the affected areas before reassembling and repeating the first bit, bend, bend, bend and bend some more. Once satisfied I'll glue shield the joint then paint the rest of the figure. I find a nice coat of sealer gets rid of the glossy effect that superglue has.

I personally like painting without taking apart the figure unless the parts are really easy to reattach, as it will happen what you described.
What I have seen most people do, is taking apart the figure (some times not required), sanding the rubbing parts off (knees, elbows, etc), reattaching the figure and then painting it.
If you still decide to paint before reattachment, I think you will need to seal the parts with a good acrylic sealant and cross you fingers the paint won´t get scratched, which I think is very improbable.
This is just my humble opinion, if someone disagrees, please guide this guy a bit more.