To update this thread as it may be beneficial for someone else.
I booked a load of flights 6 months out with my old passport details. During this time I renewd the passport and for some reason the BA system doesn't update the bookings so I always get a problem checking in. After phoning BA, the kind agent updated all my flights and said that I will be able to check in but won't be able to get an online boarding pass for those prebooked flights. Any new bookings should be fine.