Here's what MyPoints told me about old vs new numbers:
Dear bob12403,
Thank you for contacting MyPoints Member Services.
Please be informed that, you have to enter the post-merger United/Continental account number at the time of United Miles redemption (means to exchange 5000 MyPoints for 2500 United Mileage Plus miles).
Also please note that, if you have already entered the pre-merger United/Continental account number at the time of United Miles redemption, no need to worry about that, we will acquire your new United Mileage Plus number (post-merger United/Continental account number) and place it in your account.
We appreciate your understanding and thank you for your support of the MyPoints program.