Based solely on what you've shared, the optimum route is for your wife to voluntarily return to Philippines and prepare a new visa application.

Just how the ECO will apply the immigration rules cannot be predicted....the only thing you can do is to ensure full compliance with all the immigration rules for spouse visa requirements. It's so important to be totally honest and avoid any hint of deception or attempt to circumvent the rules.
That's why it's key to return voluntarily and under your own funding.

It's going to be a tough waiting game as we all know......

If all fails then that's the time you'll need to consider other options. (Which do legally exist)

Good luck