What I do, and it seems to work nearly always, is the following. I have some battery powered devices that run on 3.6 volts and I program them with the MeLabs EPIC or more usually the MeLabs USB serial programmer.

On the MeLabs USB serial programmer I pick up the 10 pin header. I only connect the Vpp/Reset, PGD, PGC and ground lines between the programmer and the target processor. I do not link the Vdd line from the programmer to the target as some chips I am using have 3.7 volt absolute maximum voltage limits.

The target is powered by it's own 3.6 volt source during the programming.

This works 99.9% of the time. Just occasionally I get an error message "target device does not match selected device" , or something close to that. This is due to poor connections or the 3.6 volt side being too low. I think 3 volts might be pretty near the limit.

HTH
Brian