Yes, when you transfer your funds from an unregistered account to a "registered account", you are deemed to have disposed of them and will realize a Capital Gain (or loss). Quite often you will be issued a T5008 for these dispositions, so if your investor hasn't provided you with a summary or other record, you may want to check in your CRA My Account and see if you do have T5008s out there.
If you don't have T5008s, you can enter these by going to Income > Investments > Capital Gains & Capital Gains Deduction Profile. Then check off the box "Sold stocks, bonds, real estate, etc ", and continue to the Capital Gains page to make your entries.
