This is the bug report I made. To me it looks more like improper reinitialisation of the BD-1 object after certain circumstances. Once it happens, you can keep dying, flying to diff planets, opening chests and he never comes back. Most people including me get it at a point where starting over would be too frustrating since there is no way to skip the beginning and it's kinda tough to have fun replaying a game when you just played it unlike when you come back to it after a year or so.
Thank you! I’ll read that report.