no matter what depreciation must be recaptured before any exclusion can be used. you face an additional issue with the rentals side because there's a special tax rule when the rental property is converted to a principal residence.
period of nonqualified use - the period after 2008 that it is owned but not used as a principal residence. (the period rented or left empty)
a simplified example
say you rented for 8 years then moved in for 2 years before the sale
your gain is $500K which includes a section 1250 gain of $100 (the depreciation which must be recaptured)
of the remaining gain of $400K, the nonexcludable portion is 8/10*$400K or $320K. the remaining $80k is taxable capital gain. also, consider that generally the exclusion can be only used once every two years.
what's the outcome if you remodel the two homes to covert to one home? interesting question. see a tax pro.
