Preface: running Jedi Academy Enhanced 1.3 + character customization mods + added autoexec.cfg in /GameData/base to enable dismemberment on pc/npcs
During the vjun2 unskipable cutscene bug where Kyle jumps into the hole in the ceiling after draining water from this room, I used the "maptransition vjun3" command to skip the level and the cutscene bug that stopped mission progress.
Upon starting vjun3 I noticed my character is invulnerable to all blasters and lightsabers but is still vulnerable to explosions, assassin droid shields, and fall damage. NPC AI also has trouble detecting my player character. Cheats and godmode are disabled.
This issue persists on older saves and new game.
Fixed, it was an issue with a character customization mod.