The game engine checks your alignment when you put your familiar into or out-of your inventory... So removing it from your bag while you are suffering from any kind of alignment change will cause it to disappear. It is also conceivable that you lost control of it while transiting areas but that’s much harder to fix because the game doesn’t save that info in your save game.
The safe way to fix this problem is to add a familiar into your inventory with sk (Shadow keeper).

Just match the type of familiar to your alignment and that should fix it.


http://i266.photobucket.com/albums/ii256/nibbit_photo/SK/pets.png

Eg. If I was Neutral Evil then I’d need a Dust Mephit

The hit points and armour don’t matter because the game will correct for this the first time you take the familiar out of your pack but you must be the same alignment as when you first summoned your original familiar. If you want to be say Lawful Good instead of Lawful Neutral then you have to kill your Ferret before changing or the game will bugout.



Wizard/ Sorcerer familiars in BG2:
Lawful Good: Pseudo Dragon
Neutral Good: Pseudo Dragon
Chaotic Good: Fairy Dragon
Lawful Neutral: Ferret
True Neutral: Rabbit
Chaotic Neutral: Cat
Lawful Evil: Imp
Neutral Evil: Dust Mephit
Chaotic Evil: Quasit