When you're done practicing, you have to make sure to reset your progress in orbit. When you first fly in, even if you leave immediately, it creates an initial checkpoint at the start of the first area. If you go to orbit after that and then fail to reset your progress before you fly in next time, you are starting at that checkpoint, which invalidates the flawless and solo run triumphs. Unfortunately, you'll have to do it again if you wish to go for the Triumph.

Good luck, Guardian! Hopefully it'll be a bit easier since you figured out tactics for the last time. Just remember to reset every time you go into orbit or before you fly in for the actual run.

That may be, if you reset from within the dungeon then flew in again, it may have saved the checkpoint as you were leaving the dungeon. I hadn't considered that, so thank you for that extra bit of thought!