The threshold is real but it is not universal, and that is exactly why your lender keeps moving on you.
Most conventional lenders use either square footage or income as their trigger. A common line is 20% to 25% commercial square footage, but some lenders draw it at income instead: if commercial rents make up more than a certain share of total gross income, the whole loan gets underwritten on commercial terms. The appraiser switching to a commercial income approach suggests your retail rents may be pulling enough weight that the file crossed an income-based threshold, even if the square footage said otherwise. That rate jump of 60 basis points is consistent with the loan being repriced as a commercial mixed-use deal rather than a residential one.
A four-over-two setup (four residential units above, two commercial spaces below) sits right in the gray zone where this happens most often. The guide for this strategy notes that managing the two components under one roof is genuinely complicated, and the financing side is part of that complexity.
A few things worth confirming directly with your lender: ask them to put the specific threshold in writing, whether it is square footage or income based, and ask which metric the appraiser used. Those two answers will tell you whether you are dealing with a firm policy or discretionary underwriting. If it is discretionary, a different lender with a written policy may give you a cleaner deal.
I want to be clear that I am describing how lenders commonly approach this, and the specifics of your loan, your county, and your lender's guidelines can shift the answer. A commercial mortgage broker who works mixed-use deals regularly would know which lenders in your region use which metric, and that conversation is probably worth having before you go further.
What share of your projected gross income comes from the retail spaces?