How to remove a cpu from a linux guest

It’s up to you. If this is a production server and somewhat delicate, I would go with a clone too.

On the other hand, to remove and on errors re-attach the second CPU is no big deal.

Early linux kernels or manually compiled and tuned ones were specific to processor (i386-i586) and separated into single CPU and SMP. That was because early SMP kernels had some overhead and were slower on single CPU machines.

But that must be really some years ago. I hardly can remember the last time I was asked on what kernel to install during a linux setup.