My question is whether card readers are preset to check if the journey of the train l’m being checked on is included. Say if I got checked on Thameslink, but I completed a GWR or a tube journey, will I still be charged maximum fare because I didnt complete a journey in the thameslink train?
As others have said, you haven't given us enough details to completely understand your query. But if you're using contactless, the onboard check is only capable of checking that your card isn't in the list of blocked cards. That might be the case if payments for previous journeys have failed, for example.
At the end of the day each onboard check is transmitted to the TfL 'back office' and their system then reconciles this against the touch in/out data to work out whether you were touched in at the time of the inspection.
If you weren't touched in, then on top of any journeys you made that day, you card gets charged a failed inspection fee (I believe this is equivalent to a maximum fare) and it counts as one of your three "strikes" in terms of failed inspections. After three strikes, your card is blocked.
Oyster works differently; the touch in/out data is recorded on the card itself so the inspectors can verify whether you touched in before getting on the train. They would likely issue you with a Penalty Fare or take your details for prosecution if the check showed your Oyster card wasn't touched in. I don't think Oyster cards get blocked for failed inspections; the idea is that you'd be penalised on the spot anyway.
