You wouldn't need to wait long (maybe a day) after cystoscopy just to make sure it all settles down, no pain remaining etc - and depending what they might / might not find !
No - its not goodbye to Class 1 if its damage from earlier stones - but lets not second guess.
I am sure you aware stones recur in a high % of cases where you have prior experience, and as part of your Class 1 you have to prove at year 5 & 7 from first appearance that you remain clear.