I'm assuming these are instructions for self tests or verification. If so, removing the instructions after they are manufactured wouldn't be easy. You can do it in microcode at the cost of making all execution slightly slower (if instruction not in [a, b, c, d]) or by physically altering the die to remove those instructions. Either way, it doesn't sound fun. It's probably easier to leave them in.

There's no reason to remove them, that's not what I'm asking. By all means leave them in, but why leave them undocumented? Explain their existence, their parameters & capabilities. If not intended for use, explain that too.

Then when something unexpected like Spectre comes along, the people that have to deal with it can say "Oh yeah, those testing instructions provide another vector of attack that our patch has to account for."

Instead we're in this situation, and I'm pretty sure there's at least a half dozen nations that would have already devoted the resources needed to uncover undocumented instructions like this, meaning ample opportunity to have developed various exploits.