There are specific requirements for registering a boat in Canada, but having paid the duty and taxes
is not one of them, as far as I know.
Duty and taxes are required to enjoy a product in Canada. The feds who register your yacht have little to do with those people who collect those funds.
I have a friend who bought an American C&C
48 Landfall, sailed it back to Canada under special license
and had it repaired by Canadian workers. He only had to agree that he would not "enjoy" the boat in Canadian waters and would leave after repairs
were done. Registration was not a problem.
There are other Canadians with boats on Lake Champlain who have special permission to even store their boats in Canada, without paying the duty and taxes, as long as they leave for the American end of the system each Spring. Again, I have been led to understand they can register in Canada.
Me, I wanted to enjoy my French-made and registered boat in Canada, and stayed totally above-board, paying a fortune. Don't blame you at all, and neither will most of the Transport Canada people you talk to.
Contact your local officials and ask questions - Department of Transport Canada, Office of Ship Registry. Hopefully, you will receive pleasant news. Try these sites: