Peter, what you did to get your PPL re-issued was a class rating skill test, not the PPL skill test. The IR proficiency check will not in itself go any way towards revalidating or renewing a SEP class rating.
There is no reason that the CRE/IRR who conducts the IR proficiency check cannot also conduct a class rating proficiency check in the same flight but they remain two distinct and separate checks (and entirely separate from the PPL skill test). It is the ability to use the IR proficiency check in place of the training flight with an instructor that is removed under Part-FCL