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The concept of fraternization only applies to officers, not enlisted members. Enlisted members can't actually be charged for fraternization.
I can conceive of some instances where they could investigate though, but this is speculation based on a lack of facts.
They can certainly investigate the relationship to determine if it began while the retired officer was still active service. They can do that to determine if they wish to recall the retiree in order to take away their retirement. They can also do so to determine if the enlisted member gave false statements concerning the relationship when it would have been an unprofessional relationship.
So, it really depends on what they are searching for.