That's weird. You shouldn't lose your permits once you've obtained them.
Even if you go hostile with the faction that gave them to you.
Have you tried actually going there? Maybe it's gone from the list by some bug (or you simply forgot to scroll down on the permits page?)
What's your current relationship with the Alioth Independents? If you aren;t currently Allied, and you don;t recall diong things to hurt the AI after you got the permit, then it's highly likely you never got his permit.
Perhaps you're thinking of Sirius?
Do missions / dump exploration data at AI-owned starports to level up, and see if it offers you the permit then.