At the time you filed FAFSA, you had to report the rental property as an asset. It’s not that the school is looking at the equity in your primary residence but in your rental property. A non-primary resident is reported as an asset on the FAFSA.
If you move back into the home and it becomes your primary residence, then, when you move, you’d request a change of circumstances and the schools can consider that for federal aid. Equity is not considered on the FAFSA. The school can consider whatever it want to award its own aid (grants, scholarships, free housing, books, travel allowance).