I went back and searched the entirety of Vilerio's Rest for her in my save. She isn't there either. Guess this fix doesn't apply to ongoing saves... and that really bites, seeing as I'm already 30+ hours into the game and there's no way I can restart now.
I'm really disappointed. It feels like a punishment for backing the game and playing it on Day 1.
Importing story fix worked, Vela does show on beach before ship repair, but where to find her later?
Guess i just need to redo character on easy and find her.
She is definitely not on ship!