A major upgrade, as you probably know, will completely remove the old
version. So, if your second installer does not write to the registry, it
makes sense that the value will be removed but not replaced. You shouldn't
change the UpgradeCode for the lifetime of the product, across all upgrade
scenarios. 

Are you using WiX to write to the Registry? What does that code look like
then? 

How have you got the minor upgrade set up? Is it a patch? Or a full install?
Does it use WiX elements to write to the Registry?
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