Is the Mystery that is active when the portal opens in Strange Remnants still useful for progressing the investigators?
A response from Nikki from FFG that strongly implies the active mystery is all but pointless once the Ancient One card flips and the Final Mystery begins (meaning that if one were to solve it, it would not add an extra clue):


  Syzygy is unique from other Ancient Ones in that it is designed to always flip. The cosmic alignment will occur whether the investigators are prepared for it or not. For Syzygy, just completing the Final Mystery is enough to win, but solving Mysteries before the sheet flips will give the investigators an advantage.