The sentence you provided can be completed as follows:

"How long did you fly from Ha Noi to Ho Chi Minh City?"

can be rephrased to:

"How long was the flight from Ha Noi to Ho Chi Minh City?"

You can also use:

"How long was your flight from Ha Noi to Ho Chi Minh City?"

These variations maintain the original meaning while altering the structure of the question.