Correct.
When they re-engined them, they were designated with the “R” after this, but no sooner were they all done than the supertrain livery appeared (1972) and a new numbering system brought in as they were repainted into the new livery. This involved dropping not only the “R”, but the class prefix letter too, and on all classes.
So what had originally been A1 - A60 became A1R - A60R when they were re-engined, then 001 - 060 only once repainted into supertrain livery. At the same time the B101, B121 and B181 classes became 101, 121 & 181 classes, and so on.