You're fine. Just keep sending the inquiries until you get your new case number. Do not worry about the expiration date. It will be automatically extended. You should get a K1FTP email, not a physical letter, when your case is sent to Manila. On CEAC, you will select immigrant visa to check your status once you know your new case number.
You can work on the DS-160, but you will need your MNL case number to complete it. The website will save your entered information for a month. Each time you access it, the one-month period starts over.