Duplicate vs. replicate vs. reduplicate

If you replicate a finding, you may have come to the conclusion independently.

If you duplicate a finding, you have not come to the conclusion independently but have restated it.

Reduplication should be used only when something has been duplicated more than one time. If something has been duplicated exactly once, it is simply duplication.

Since your example sentence mentions "identical copies," duplication is more applicable than replication. Reduplication could be used if the procedure replaced the same nodes more than once but that doesn't appear to be the case here.

Replicate is used in the following sentences, where duplicate should not be used.

It might be impractical to replicate eastern culture in the west.

Interleukin-16 prevents the virus from replicating itself.

These findings have been replicated by Atwood and Jackson.

When talking of genetic material, or a living organism, you don't say duplicate except in the case you mean double as in "the normal amount of DNA has been duplicated thousands of times."
When talking of scientific experiments, you could say "their experiment duplicated work already done," but in that case duplicate would mean "do something again unnecessarily."

In the example you make, I would say the nodes are duplicated. Re-duplicated would mean "duplicating something that duplicates something else": I duplicate node A to create node B, and I duplicate node B to make node C.

Here's how I look at it, but I could be wrong.

Duplicate: To make one exact copy of something.

Replicate: To make a general copy or copies of something, one or more times. ie: a printed copy of an original painting. (Make a replica)

Reduplicate: To make one or more exact copies of a duplicate. To make more than one exact copy of something.