Were El and YHWH ever considered by ancient Israel to be in a Father/Son relationship? Were El and YHWH always identified as one and the same god by Israel, or was that a later development?
As with many other topics, the Bible is far from a unanimous voice on this. Depending on the OT author (and on the time period) you can read contradicting opinions about Jehovah’s relationship to El. Some OT authors (ie. the burning bush scene) claim that Jehovah and El are one and the same. Other OT authors seem to differentiate them.
For example, Deut 32:8-9 is interpreted by Simon Parker, Margaret Barker, and Mark Smith to mean that El (the father) gave Israel to YHWH (a son). Heiser interprets the passage to mean that YHWH is the head god doling out nations, and he saved Israel for himself. As of last year, Bokovoy agrees with Heiser on that point.
Based upon this evidence, Heiser’s assessment of the view featured in the current form of Deuteronomy may be correct; however, Heiser ultimately fails to address important evidence recognized by many contemporary biblical scholars that suggests that Israelite theology did in fact evolve in a manner consistent with the basic claims of Parker and Smith.
From my reading, the debate among scholars is not really about whether or not YHWH and El were at one time recognized as distinct deities by Israel. That they were distinct in Israel’s early history is basically agreed upon by most scholars. Rather, the debate is about how that relationship transformed into the later understanding of YHWH and El as being one and the same.
Israel’s understanding of El and YHWH was an evolving one. Their theology was not static or homogenous. The form handed down to us by the final redactors of the OT represents the thoughts of only a few particular generations, and should not be understood to represent the majority of Israel’s long theological development. Because the theology of Israel was an evolving one, it makes sense that the OT demonstrates an evolving theology.
John Day has a very specific chapter in his book “Yahweh and the Gods and Goddesses of Canaan” which starts out saying, “Were Yahweh and El originally the same Deity or not ?”
That should be enough reading to get you started.