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OK, I see the reason for the save(). It seems as though all pull requests are serialized by job in a giant hashtable which is stored in org.jenkinsci.plugins.ghprb.GhprbTrigger.xml. It seems unnecessary to store state which is already stored externally, but perhaps this is a design decision which is too deeply baked in.
So perhaps the fault/fix is in jobConfigHistory plugin and it's duplicate history detection.
One can work around the issue by adding GhprbTrigger to the pattern's in the jobConfigHistory's "System configuration exclude file pattern" in the Advanced area of the Job Config History plugin.
I'll close this as I suppose it's hard to argue that this is actually a defect in this plugin.