Then you should be fine as you applied before your wp expiration date
Here is my experience:
I didn't bother extending my SIN since September 2017, when my study permit expired. Just used the expired paper. I had a valid 3 year pgwp and my employer didn't care about validity of sin since I had a valid open wp (of course that depends on your employer). And I never had any issues either with filing taxes or with CRA.
Also, my wife applied for wp extension 2 months before we got passport request. We landed together with zero difficulties and she was on implied status at the time of landing. Just be aware that when you mail your passport(in case you aren't from a visa exempt country), Ottawa processing centre will issue COPR and stamp your passport with a single entry immigrant visa that can be used to re-enter Canada.
We also asked the border officer to withdraw wife's wp application, but he said he couldn't and we would need contact CIC to withdraw it, and we contacted CIC via "case specific inquiry", there is a special section in drop down menu called "withdrawal of application" or something similar to it. After a couple days we received an email stating that a comment was added to the wp application and it will up to the processing visa office to withdraw the wp application and possibly refund some fees.