You have a win-win situation here, so I don't know why you are panicking. As long as you have sent the passport to the correct address, then it's just a question of responding to the email for FSW PPR letting them know the situation. At least all immigration visas processed in Ottawa are issued in one place - so whether your passport was sent for CEC initially or not, they will end up in 365 Laurier Ave West.
I think they should already have your passport and have even moved your files around, especially now your ecas has been updated. But you still do need to respond to the FSW PPr stating the situation
I imagine the decision on which application to withdraw depends on a lot of factors even though it should rest with you. But besides that, the VO can exercise his/her discretion depending on what they feel is best for you. They may also consider the fact that your FSW2 was filed first.