1. The small trading company took in a lot of money from trusting investors and then closed up. It had been a fly-by-night operation.
2. Although Darlene had been working for the company for a few months and they had paid her, she still didn’t trust them. She felt she was working for a fly-by-night company.

The expression suggests the idea that the operation closes up and flees under the cover of darkness rather than in the clear light of day.