Although I have to say, I have no experience of FLR myself, since my wife would be applying for ILR, really FLR should be a formality for you, as long as your application is in for FLR, I see no reason for your dearest and nearest to worry, she defnately should not be worried about staying here in UK, she is legal, there are about 30,000 Filipinos in London alone who are illegaly working and living undocumented, so your wife certainly should not be worrying, tell her, as long as the paperwork and application is sent before the expiry of your existing visa, it should be done normally 30 days prior to expiry, then you just sit it out, until its returned.
Hope that is of some comfort.
