If i choose the Bonded Witch, the book indicates that I will lose the Familiar, but does this imply that I lose the Patron's spells and they are replaced by those of the object?
No, you keep your patron's spells as normal. The spells of the bonded item are a bonus, just like a wizard can cast 1 spell per pay with his bonded object.
Check the Wizard's Arcane Bond class feature.