After the consultation period was over the council wrote to us saying
there
had been no objections but he (the planning officer) would not approve the
scheme in its current form and so we had to make some major changes to the
design.

It sounds as though the application is being dealt with by the planning
officers under delegated powers. This is quite normal and if you don't make
the changes then it will be refused.

We only just found out that the planner was happy with the changes but
they had received an objection from a neighbour about the 1st floor
window which the planner considers to be a valid objection. However,
since
we are only two working days away from the final decision, it is far too
late for us to amend the plans.

As above if you will not amend them then it will be refused.

My question is: Does anyone have any ideas how we could avoid having to
resubmit the planning application and start the whole process off again?

As above

Also are objections received after the consultation period finished valid
anyway?

Objections can, and indeed frequently are, made right up to when the
decision is made. Often this is at the planning committee meeting where the
matter is being decided. In the same way applicants can submit amendments at
the last minute. Objectors have rights just as applicants do. The deadline
is not cast in stone since you can ask for it to be deferred pending
negotiation over the changes or withdraw the application entirely. In the
latter case you can submit an amended application and go through the whole
procedure again without paying again. Your best bet is to ask for it to be
deferred and negotiate with the planners. If you decide, as applicants often
do, that you want is decided as submitted then you will almost certainly
lose and have to pay again for an amended application.