Its what Cas said - As I understand it the Brera S was modified to the S spec at the docks in Bristol using a kit of parts applied to a pretty bog standard Brera.
When sales were disappointing, there was a time when it looked like they would be stuck with a load of unsold cars - so some of the S kits were partially split and sold off as accessories - hence some wheel sets appearing on eBay. It also explains why standard Brera wheels with delivery mileage were available, as they came off the donor cars.
They are now presumably finishing off the "end of line" cars in preparation for the TBi coming in - but haven't got the right number of full S kits anymore - hence you get the half-breeds.
I don't think any cars were converted back from S to standard spec - more like they were never converted TO S spec.
What lies beneath? Anyones guess - you need a ProDrive build spec and tick off the bits you've got, and negotiate over the bits that are missing.
PS - if you own a genuine S it must now be worth more as there will no longer be 500 made