I think there is a good chance you will be ok OP. These are my reasons:
They have been there a long time and no one has complained.
Enforcement if it were to be considered has to be proportional and justified. If the breach is long standing, not hidden, and not undertaken by you there is a reasonably high probability that it would not meet the LPA's threshold for enforcement.
Finally and most importantly the onus is on the local planning authority to prove breach. Your listing says 20th century windows. This means the windows at the time of listing were not themselves original.
This is important for two reasons. First it is relevant to any decision to enforce (they can't make you do anything more than replace what was there before - and they may have been hideous prior replacements).
Second and more important it would be open to you to say that as far as you are concerned the current windows are the windows that were present at the time of listing. The burden of proof is on the council here. So you would be saying that there is no breach.
The council in my opinion are not going to spend a lot of time and trouble on some historic forensic exercise to find out what the windows actually looked like at the time of listing and try to force you to reinstall them.
So I reckon that, while no lawyer will give you a clean opinion on this, in practice I don't think you have too much to worry about.