Doing my usual trawling of the web for any prototype information and I hit a assemblers thread about the Zelda Oot master quest debug from last year and there was a lot of talk about it being fake. Now a well respected member of the n64 community stated his distrust in the prototype and claimed and I quote

"Some people use gangwriter with beta/unreleased game rom that can be found on the web and resells "outstanding" protos.I heard many bad stories about them and I am afraid it won't be the first or the last one."

I've scoured the web to find evidence of this but I haven't first hand seen anything about this ever happening.

Now that is the criminal side of reflashing. I got thinking then if you had a prototype cart that was damaged but the Rom was intact would it be morally wrong to dump then reflash it onto another cart? If you bought a prototype Rom then flashed it onto a blank cart would that seem less desirable than the actual cart that was flashed by the developers? I'd love to hear the opinions of those who collect prototypes.

The best option in your example would be to put the newly flashed PCB in the shell that housed the damaged prototype, even if the shell is broken too. Also keep around the bad PCB, in case you were ever to sell the game. Being honest is the quickest way to counter suspicious parties.

This is purely theoretical but that is a good idea.
I was talking to a fellow collector and they brought up the question how would you feel if...? Just the thought of someone reflashing carts just makes me a little uneasy. A Rom flashed by a collector does not seem anywhere as special as one flashed by the developers.

I have been feeling this way with some of the NES "prototypes" out there nowadays... a basic shell with just a basic label [sometime masking tape or a vhs sticker], a normal game pcb with eproms flashed with a "prototype" rom.. soo easy to fake it.. Anyways concerning the N64 ones, I could definitely see this being the case now or in the future.

I guess its been a problem with EPROM's for a while now, a lot easier to reflash.
lucky for the n64 the hardware is incredibly hard to reflash.

Think if a SNES proto was being the system proto in question people wouldn't second guess at it. If a SNES proto rom worked on an emulator but failed to work on a SNES dev board, the board could be damaged. If you swapped out the eproms onto a new board and they worked in system now it would be no big deal. In sense you are doing the same thing but the physical rom when removed from a N64 dev board can not be held like the SNES eproms. Like mentioned keeping the old corrupt/damaged proto with the newly flashed proto would be best. Also being 100% upfront on what was done is also important. With everything collectible you have to worry about frauds and fakes. Really a matter of knowing as much as you can on what you are collecting and having trust in your seller. The average person doesn't have the capabilities or means to flash rom to physical protos.