I would say the amount I had saved is under £1000, I’m really worried as I keep reading stories I know I’ve been stupid and more than happy to pay a penalty or the amount I owe them
This could be very expensive for you. Let's do the maths.
Suppose you've saved £1,000 (I know you say it's less than that, but it keeps the maths easy). That means the full price tickets would have been £3,000 (and you paid £2,000 with the discount). However, it's standard practice for the rail companies to ask for the full price without any discount for the amount you've paid. That would mean they would come after for you for the full £3k. (Sometimes they are more generous when it was more obviously a mistake, such as a railcard only recently out of date, but given there was clear intent here, I wouldn't bet on it.)
But... they also usually charge a full anytime single fare for each journey taken, whereas you are likely to have bought off peak or advance tickets. That could make a huge difference.
As an example, an off peak day return from Bristol to Paddington is £95. But an anytime single is £126. So for the ticket that you saved
£30 on they
could ask for
£252, so a factor of eight. That's probably an extreme example, and it all depends on what journeys you were actually taking.
If you do get offered an out of court settlement, you'll be expected to come up with the cash pretty quickly, so you might want to go through your list of journeys and get some idea of what a worst case scenario might be. BRFares.com lists all the available fares if you need to know what any particular fare would be.