Is it your passport itself expiring, or just your status in canada? If you mean your status is expiring, since you applied before your status expired you have implied status until a decision is made on that extension.
I had a similar issue, we initially sent in my PR app in March, I applied for an extension (visitor record) in April, my PR app was returned in May because I forgot to include my birth certificate. I resent mine immediately, and my Visitor Record was approved early July, long before my PR app started processing. I personally don't think it will be a problem as long as you are in the process of getting that application submitted.
As far as waiting to resubmit...here's the thing. If you resubmit and they deny your extension, you'll have to leave Canada and apply from outside the country (your Inland app would be invalid because you didnt maintain legal status in Canada). You can wait, it just means you'll be waiting longer to get your OWP (if you've applied for one).
Either way, once your initial status in Canada expires in the next two weeks, you can't leave the country until a decision is made on the extension
