Getting approved to refinance 2018 while 'taking a loss' in 2017

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Without going into the weeds on the 'why', Last summer I quit claim'd a non-performing rental (Mayflower) taken Sub2 (with a basis of $65k) back to the original seller, in exchange for them forgiving $42k in notes for 4 other properties purchased from them, due to them in 2020. I then immediately sold one of those other properties (Kingsbury) which previously had a note due for $27k, and walked away with a check for $37k, all other variables aside, I assumed that i made a profit.

Fast forward to tax time / refinance time, my accountant is telling me that the profit from Kingsbury, was actually a loss associated with quit claiming Mayflower back to the sellers. Even though i physically took in $90k from the sale of real estate in 2017, my taxable income is $20k.. which by tax returns alone, looks like sh!t compared to the previous two years. I'm perfectly fine with paying less taxes, but my concern is my ability to cash out refinance my rentals and buy a personal residence this year. 

My question is, do lenders look only at the tax returns, or would they take the circumstances/HUD-1s into consideration when approving loans?