"For some reasons I decided to live in property B and treat it as a main residence."
You determine the treatment of your home as your main residence on your tax return in the year of sale of one of your properties. Not before.
Treating former home as main residence | Australian Taxation Office
From link
"Usually, a property stops being your main residence when you stop living in it. However, for CGT purposes you can continue treating a property as your main residence:"
Once a CGT event occurs then you determine how you want to treat your property.
If you treat property A as your main residence for your whole ownership period then it will continue to be your main residence as under the guidelines in the link. There is no requirement to move back in before the 6 rented years are up.
Be aware property B will be subject to CGT for your entire ownership period if you choose this option.
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