They do?
How are you certain only one or two cylinders would be misfiring?
Certainly I'm hoping none of them will. Structurally, we have designed the stress-loading to compensate for an occasionally underperforming thruster. I believe in over-engineering to accommodate room for Murphy's law.
The Gas-Cooled Nuclear Reactor/Rocket Engines will all be brought up to operating temperature in their commissioning stages. Any engineering failures or component shortcomings should be disclosed and corrected at that time.
As power sources, these devices will be cycled around, providing the on-site power for our hydroponics bays, on-going construction programs, incipient laboratories and production facilities, ordinary lighting requirements, and for purely testing purposes as well.
They will also be tested as rocket engines, usually at reduced thrust. Our pre-flight checkout procedures will be as thorough as possible, and on launch day, we're hoping there will be no failures at all.