Not working with Atmel m yself, I have a recollection from a post somewhere of a bit? that must be set as part of the ISP or the chip will stay in boot mode.

Is it Atmel that program while the chip is held in reset?

What is most often different between chips and their 'recommended replacement' is related to programming and clock cycles.

Not much help, but have a reread of the programming instructions of your new chip and FLIP

Erik