Could still be Declan's baby - the time she was sick with poisoning could have doubled as morning sickness and those pregnancy tests she took could have given an early negative reading. Or - that last night they spent together at the cottage could have been the time she fell pregnant. It then opens it up for Declan's return at a later date once he finds out he has a son. And if it is Declan's there is no way Charity would want Declan finding out he has a child, so she would rather name someone else as the father. The timing also works - September/October to June... she was still with Declan 9 months ago...
Was the baby prem or full term? We're still a couple of months behind the UK in NZ so won't see these episodes until August.