This sounds like the answer. Thanks! Specifically if a 
JDOOptimisticVerificationException is guaranteed when updating a deleted 
entity. 

So it looks like my confusion stemmed from misunderstanding makePersistent() 
and  believing it was need for updates.
The tip about putting obj = getObjectById() & obj.changeSomeValues() inside 
a transaction also clarifies yet more for me.

A question about the "ancient version of DataNucleus" you mention:
Is there a more up-to-date approach I should be using within GEA? Could you 
point me toward the resource for that if any?

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