I had to tackle a similar issue while programming the AMORE package. I recommend you to have a look at the source code of its "copynet.c" file. You may find useful the reading of the "copynet_RC" function ( Copies the SEXP net to the *ptnet) and the "copynet_CR" function (Copies *ptnet to SEXP net).
Of course, I do not pretend to establish what best practices should be, just to show you how I solved a similar issue following my personal understanding of what was appropriated in that situation.
Best wishes and Merry Christmas!
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