1) If the Form 1099-S, that is reported from the Title Company shows the sale price, and then payment of 'debt' related to the sale, and the gross proceeds are essentially $0. Would this mean we have no gains?
No, not necessarily. It just means that no physical cash (or check) for a positive amount was paid to you directly, at the closing. Seems no two closing agents handle the 1099-S the same. Any gain on the sale that was used to pay off the balance of what you sold is still gain to you. Sometimes I've seen the payoff amount included in the 1099-S. Other times I've seen it not included. So you should not trust the 1099-S numbers at all. (my opinion.)
would we be able to reinvest those gains within the 2 year period to defer the tax owed or go back and amend the tax filing to recoup those funds??
No. that tax rule was eliminated over 20 years ago. What you do with the gain does not matter. If it's taxable, you pay taxes on it. Period.
