Did all the posters here miss the main point of the original post? He doesn't live there anymore!
Your new house is your principal residence. You are going to have to pay capital gains on your former residence as it no longer classifies as your residence and simply as a rental unit.
Amazed that only one poster picked up on this.
Didn't miss it. The question is not "is this my principal residence?" (which it is clearly not) but "what is the impact of the capital gains tax when I sell this property - can someone explain?" People responded to the question being asked.
He will owe capital gains tax on the portion of the building that was always a rental unit. (If he has been claiming CCA that will complicate matters further, as to what the capital gain is.)
The Principal Residence Exemption from capital gains tax on the other unit will be pro-rated for his period of ccupancy. Given that he moved out only a little over a year ago, the exemption will still be nearly 100%, as the formula is:
(No. of Years as Principle Residence + 1)/(No. of Years of Ownership)
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