These may be separate issues. It sounds as though your state allows the fees because other lenders are charging them as well. Likely you are good to go.
State laws set the usury rates. My experience is that the OCC follows Federal laws, and recognizes interest rates, but isn't intimately familiar with the "ins and outs" state laws can impose on different types of loans and under different circumstances.
So I wouldn't rest on the fact that this has been ongoing, but rather that you had competent counsel review it thoroughly. As noted, I'd watch and document the waivers as that is the tricky area you must address here.
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AndyZ CRCM
My opinions are not necessarily my employers.
R+R-R=R+R
Rules and Regs minus Relationships equals Resentment and Rebellion. John Maxwell