I don't know why you left your wife's passport renewal so close to the required time to apply for ILR. It would have been better to apply earlier. Did you at least take a copy?

In the case of our recent FLR-M application there was a question about whether or not you can supply the passport and if not state reasons why. You might be better off stating that it hasn't arrived if it doesn't come in time. Did you get a receipt for the passport application from the Philippine Embassy? Maybe submit that as evidence with a note you will supply the passport as soon as it arrives.

I would get specialist advice if I was you. You can't in any circumstance let your wife's visa expire.