What is the difference between the names, Yehonatan and Yonatan? How is Yehonatan pronounced?

ב"ה Shalom Yonatan and Yehonatan are used interchangeably in the Tanach. As a matter of fact , in Shmuel 1, 19:1-2 both names appear in the psukim consecutively. When reading the Tanach one must make sure that he reads the names as written, Yehonatan or Yonatan. Some people give one name or the other to their children in particular and they expect the name to be pronounced as given. Some have a preference to Yehonatan having 3 letters of Hashem's name, and some tend to avoid that form of the name for the very same reason. The Radak on the above pasuk says in the name of the Mesora, when the change of the name in the Tanach took place and the exceptions to the rule. Shabbat Shalom and all the best.