Yes, unfortunately this glitch was still present in this release after being reported and thought to be fixed prior, but was reported again. Apologies!! Thankfully, though, it has been fixed with the latest dev version of the game and won't be present for the full release of version 3.0.
As long as it allowed you to get the Green Jewel, the save should still be salvageable, but you'll need to use a secret space found across from the Blue Orb's pedestal in the Hall of Orbs in Gianna Castle. Interact with the wall opposite and you should get a prompt offering to restore any lost party members. Again, apologies for the inconvenience!