Philippine passport + taiwan passport what to do ? please help...thanks

Good evening guys, i have a question for a friend, these are the basic information she has

  1. she has a taiwan passport but she does not have taiwan ID
  2. she also has a philippine passport
  3. she came to taiwan to rest , she has been here since last December, she has an entry permit(3 months extend for another 3 months stay in taiwan) on her taiwan passport, but has a visitor’s visa on her philippine passport (15 days)
  4. when she came in taiwan, she only have entry stamp on her taiwan passport.
  5. if she plans to go back to the philippines now, will the philippine immigration look for trouble because she only has entry stamp on her taiwan passport and not the philippine passport?

I am not sure if this is clear , but please advise anything you know regarding this , thank you .

I dunno about how they do things in the Philippines, but I used to travel leaving with my TW passport, and entering other countries with my US passport. Neither immigration dudes from Taiwan or the US gave me any trouble.