It sounds like you are re-inventing the wheel a bit here
Duality serialization already takes care of object identity (reference A twice - serialize two references to A instead of A twice), so if you use the builtin Serializer
API, that shouldn't be an issue.
(There are of course good reasons for re-inventing the wheel in some cases, so I'm just mentioning it in case you simply didn't know you could use them for your own purposes.)
Is there something about PCL's, duality, or something I'm missing? I could come up with my own unique ID generating algorithm but I'd rather use what's tried and true before rolling my own.
As far as I know, there's nothing related to Duality or PCLs that would cause Guid not to work anymore - in fact, Duality uses that same API as well
for providing version control stable GameObject IDs, so my guess would be that the error is somewhere else.
Maybe you could share some of the relevant code for us to take a look? Ideally in a minimal, self-contained sample that reproduces the issue.