There are many people who think that John is a shortened form of Jonathan. If that were the case, one might wonder why Mattathias, the father of the Maccabees, had children named both John and Jonathan (1 Maccabees 2:2-5).
John comes from Hebrew Yohhannan and means "Jehovah is merciful." Jonathan comes from Hebrew Yohnatan and means "Jehovah has given (a son)." They are not the same name and were not interchangeable.