Team Win Recovery Project (TWRP) is a popular alternative recovery used by those who like to root and modify their Androids. A new thread on Reddit asserts that Pokemon GO will not work if it detects signs of it in a device's storage. This behavior may be intended to prevent cheating in this augmented-reality (AR) game.
https://www.notebookcheck.net/Pokemon-GO-reportedly-blocks-players-using-Android-custom-recovery-or-backup-methods.454285.0.html