Well this is quite tricky.

When your wife lost her passport, didn't she inform UKVI? Did you report it to the police? I'm not sure if she can apply for transfer of visa to her new passport or apply for a BRP while in the Philippines. You can probably check this https://www.gov.uk/transfer-visa. If UKVI would check her details in their data, they can see what visa she has and her right to come back here.

Also, you should call and inform UKVI as soon as possible regarding your wife's situation. They can probably help you better with regards to the process you and your wife can do.