I don't think she has got anything to worry.
If there is any trouble to be faced... it will be her local husband. So let her talk to him so that he can resolove the issues with government official.
As long as she is under the sponsorship of the compnay that is owned by him and she has the marriage certificate issued by Philipines government, she will not have to take much trouble... it is her husband who should be worried and needs to find-out a soluation.