Scenario 1 : Only Pcell has PUCCH Rx. like Rel10 UE's
This is Quite possible scenario in LTE. UE might miss the Scell PDCCH and reads only Pcell PDCCH. Decoding problem eNB cannot avoid because it is depends on the UE channel condition. Pcell can configure the overlapping HARQ/NACK resource such way that Pcell at least receive the PCell HARQ feedback irrespective of PUCCH format. Basically N1PUCCH resource will be the key to configure.
Scenario 2: Scell has PUCCH. Above Rel10 UE's
This scenario is easy to detect. Scell eNB treat this as DTX and does Retx.