If the present fund value is less than the total invested amount in NPS-Tier 1 account and we change the scheme preference(I mean change the % allocation in Scheme E,G,C) then do we have to book losses?
No taxes are not applicable when you change the funds allocation.
Yes you are booking a notional loss in anticipation that reallocation will give you better profits compared to staying invested in same allocation. What will actually happen can't be predicted.
Yes that is correct, you redeem at current value and switch to new allocation.