To my knowledge, issues come with the so-called "abstract" graphs from OcamlGraph in which vertices have unique ids.
1) if there are abstract vertices in RAM while unmarshalling some others, you have to be sure that RAM vertices do not share ids with unmarshalled ones (except if you really want that).
2) Before creating new abstract vertices, you have to set the global id counter Graph.Blocks.cpt_vertex in the right way (by marshalling it and by calling Graph.Blocks.after_unserialization after unmarshalling).
I'm not aware of any other (un)marshalling issue with OcamlGraph datastructures.
Beyond OcamlGraph, similar issues potentially exist for any datastructure which uses unique ids as keys and/or hashconsing techniques. For instance, a quite big job is done for solving this issue in Frama-C (
http://frama-c.com) which uses many hashconsed datastructures (included abstract ocamlgraph vertices, but only the above-mentioned issue 2 applies in the Frama-C context)
Hope this helps,
Julien Signoles