I filled out an online DS-11 and DS-64 online, but I have now found the passport. The application has not been executed but I am afraid that the passport may now be invalid because the?application was completed online. Is there a phone number or email for them to contact and confirm the validity / cancellation of the current passport?

You can call National Passport Information Center at 1-877-487-2778 and request that a specialist verify the status of your passport. Most likely though, if you already submitted the DS-64 online, then it is invalid in the system. You will need to apply for replacement of Lost/stolen PAssport.
You should submit the recovered passport with the DS-11 at an acceptance facility, and can indicate on the DS-64 that the passport was thought lost but then found after it was reported.