My character made it to obtaining the Cowl and head the Thieves Guild but when I tried to check in to the Arch-Mage quarters (my character was Arch-Mage) I could not get into the University and the faction was no longer listed in the stats. Did this happen to anyone else?

The only thing I can think of is that you must have done something to be expelled. Check your quest log and see if you have a quest requiring you to pay a penance to rejoin the Mages Guild.

Aero

you probably got busted when you stole that ice staff??

it probably wasnt that u got caught stealing the staff casue thats easy but did you kill that mage who had the arrowhead, cuase hes a member of the mages guild and i killed him and had to get back in

When you wear the Cowl, you essentially become a different person. You ARE the Gray Fox.

To fix it, just take off the Cowl. You'll be back to your normal self.

If you ever want to commit a crime, I suggest you use the Cowl. It's pretty useful.