No, the fact that your renters didn't pay the rent they agreed to pay doesn't affect your answer about whether the property was rented at a fair rental price.
The purpose of this question is to identify people who rent to friends or relatives at below market rents so that they can get a tax loss. If your intention is to get a fair market rent, you can answer that question Yes.
As far as rental days, you should count all of the days your renters stayed in your property, but not the days that squatters were there.
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