That's probably why, when you paid the loan your cash dropped and your airline lost some liquidity. Especially if you used most of your cash on hand to pay the loan. A drop in cash affects the debt/asset ratio, and if you have a lot of debts (aircraft leases, gate leases, and so on) and very little assets (owned aircraft, cash) that ratio can get turned in the wrong direction.
I am the developer of Airline Enterprise