Hey there, unfortunately you are correct, going back to orbit and returning will break a flawless run. The game does not store the flawless or solo state of the checkpoint, so a flawless run has to be completed in one single run. The emblem trackers may track different things, like personal deathless completions, or count checkpoint runs as full ones. But the triumph does not.
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Thank you for clarifying. I would understand if I exit for whatever reason, but the bug made me do it and I wouldn't exit otherwise. And I also had a message that I ended it solo flawless. That's kind of strange I have to do X more runs because of that.