You can (I have) get and keep a familar different then what you are supposed to have. What you need to do is rename your familar's creature file. You dont have to edit anything, just rename it.
The problem with messing with your alignment, the familar is actually two things. Its a creature and an item. Sometimes when you switch a pet from you pack to the ground, it will disappear (or just change to the natural familar for that alignment).
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