You will need to speak to an accountant about the cgt implications.
Cgt may apply, it depends on the acquisition value and the disposal price and whether any available relief(s). One thing you can do is ensure that you own the flat as tenants in common. This means that you will have separate and distinct shares and each owner can then make use of their annual exempt amount.
Have you considered the stamp duty land tax implications?
Under the new scheme your purchase would be subject to the additional 3% surcharge because at the point of purchase you already own a property. However, you can claim a refund of the surcharge if the flat is sold within 3 years of the purchase of the second property.
To avoid cgt and the Sdlt surcharge you can sell the flat simultaneously with the purchase of the flat. No need to pay additional taxes if you do not have to.
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The mortgage is irrelevant. Your sale must complete on the same day as your purchase, if not you will be caught by the surcharge and will have to pay the additional 3% Sdlt.
There will be no cgt if you complete the sale and purchase on the same date, provided that the existing flat is your principle private residence.