According to the rules of familiars the following applies to saving throws
Saving Throws: For each saving throw, use either the familiar's base save bonus (Fortitude +2, Reflex +2, Will +0) or the master's (as calculated from all his classes), whichever is better. The familiar uses its own ability modifiers to saves, and it doesn't share any of the other bonuses that the master might have on saves.
My wizard has Fort 1, Ref 2, Will 3 and my familiar (a Compsognathus) has Fort 4, Ref 0, Will 4. Does that end up with Fort 4, Ref 2, Will 4 for my wizard?
My familiar has Fort +4, Ref +4, Will +0. Does the rule mean that the familiars save bonus changes to Fort 2, Ref 2, Will 0?