Hi Jelle,
From the javasource, you can see that a comma-seperated value is expected, similar to membersToSkip and membersToKeep
From the documentation of the Mendix DeepClone Java Action, you can get the syntax for a single input:
So I would expect you would need something like this:
ModuleA.Entity1_Entity2,ModuleB.Entity1_Entity3
I didn't test this, but hopefully it works for you.