Yes, of course - it's possible to recreate the functionality of chips in an FPGA for example. People tend to do that at a system level more than a individual chip level, but I suspect in years to come that's what we are going to see more of with some systems. For example the CIA or VIC chips in a C64 are a good candidate, and I think someone has created a SID chip in FPGA form, and there was a similar product called the Nano SwinSID which emulated the SID chip in software but can be plugged in to the board to replace the actual chip. It might be a bit trickier with the Neo Geo custom chips because of the package types used (all SMD), but its totally possible.
I've also seen people 'attach' custom logic that they've designed to 'patch' failed internal logic in the chips. I was going to do the same thing when my Neo-C1 failed but it was just easier to swap the chip at the time. I have seen someone do that on YouTube though, they some partially failed address decoding logic (in the C1 I think), and they bolted their own 74 logic onto the top of the chip, routed a few wires, cut a few traces and they managed to get it working 100%, despite the chip having internal faults.