Use of Rf_duplicate

PROTECT(y=x); and

This has no sense as y is just the same pointer as x. By doing this you 
did not create any new data, if you modify y, x will be modified. y does 
not need protection as x is probably protected.

PROTECT (y = duplicate(x));   ?

This will allocate new memory for data in x and copy data over there. 
This is correct, modifying y will not modify x. And y needs protection 
as it is newly allocated.

PROTECT(y = duplicate(x));
PROTECT(z = duplicate(VECTOR_ELT(y,2)));

It is not clear what you want to achieve by this. z will not be part of 
y any more

PROTECT(y=duplicate(x));
PROTECT(z = VECTOR_ELT(y,2));

The correct way would be

PROTECT(y=duplicate(x));
z = VECTOR_ELT(y,2);

as you do not need to protect z, it is done by protecting y

And if I did create a duplicate, is there a way to destroy it manually
before the end of the function, rather than rely on on the R garbage
collector?

Not that I know about.

Best,
Oleg

Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466