Would you care to post the redacted text of that email here, because what I have seen in writing from HMRC says that if you settled a scheme and did not explicitly declare the other years (from the same scheme) as part of that settlement (i.e. they were aware of those years) then you will be hit by the loan charge. I have seen settlement agreements that explicitly list closed years (from the sane scheme) as part of the agreement. - I guess these are ok.
If you used other schemes not covered by your settlement, then you will definitely be hit by the loan charge. For example , you could not settle Sanzar and then expect Edge (unprotected) to escape the Loan Charge.
It's HMRC they make the rules up.