300mm F2.8 Non IS

I have read that this lens posses an AF motor which is irreparable. My question however is regarding the fly by wire system.

If the AF motor fails, does the manual focus still work if the lens is hooked up to a camera?

That's the way I read it, but mine is still working so can't really say for definite.

Electronic manual focus is probably a more useful term than the correct fly by wire.

It's the manual focus function that is different from non fly by wire.
Normally there is a mechanical connection between the focus ring and lens elements that need to move for focus.
Your lens does not have that connection.

If your AF motor fails it's repair or get your subject to the now fixed focus distance.

Yes, AF motor is irreparable. Manual focus doesn't work