Hi Dan, welcome aboard!
Yes, since she has been away for over a year, her permanent residency is considered to be abandoned.
IF she had originally intended to return to the US within a year but unforeseen circumstances made that impossible, then she could file a petition as a “returning resident†at the embassy in Manila. That would be the fastest way and it will cost $400 to try it. But from your explanation above, she would likely be turned down.
That leaves you with the option of re-filing an I-130 spouse petition from scratch. But keep in mind that you will probably have to go back alone about 3-6 months in advance of her visa interview to establish U.S. domicile.
I would contact the Homeland Security Office at the US embassy in Manila and see what her current immigration status is and then take it from there.
http://manila.usembassy.gov/wwwh3206.htmlAlso, the Immigrant Visa Branch can give you more info:
http://manila.usembassy.gov/wwwh3234.htmlDo you have any kids over there?
Ray