This is one instance where wild speculation can only cause you too many sleepless nights.
Employee loans are a "class" or "type" of loans. Only loans of a similar class or type are compared with each other, so Employee loans would be compared to other Employee loans for a Fair Lending review.
Now, if you have similarly qualified employees, and one got a more preferential rate that the other did not, and the only difference is a prohibited factor, then you may have a problem.
Generally speaking, most institutions would not have enough Employee loans to be considered for a separate Fair Lending exam analysis. Or put another way, the amount of employee loans pales in comparison to the amount of Mortgage loans, or HELOCs, or auto loans, or credit cards.
The Fair Lending exam procedures are based on the relative risk for fair lending issues. Absent any glaring evidence of overt discrimination in policy, advertising, or complaints, the higher risk is going to be in those portfolios that are larger.
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CRCM,CAMS
Regulations are a poor substitute for ethics.
Just sayin'