The LOL should not affect the APR because no fee is passed on to the customer, your disclosing it correctly on the GFE and HUD, however those are RESPA and APR is Reg Z, so if your software doesn't figure that out for you, you may have to go in there manually and tell it not to affect the APR, We had this problem too, but fortunately for us it's as simply as checking a box.
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The higher up the monkey climbs, the more you see of it's behind.