This is just pointless now. The rules clearly state that specific trumps general, and "counts as a ranged weapon when thrown" is more specific than the general rule of "it's a melee weapon". You choose not to see this though, and can show evidence supporting that assumption beyond the general rule. If you're going to ignore the specific trumps general rule the go ahead, but it doesn't make what you're trying to do correct, and it causes a whole host of problems with other specific rules that trump general ones.
We are arguing that "counts as ranged when thrown" and "melee" are orthogonal concepts. They simply do not interact. Which is good, because if they *did* then a thrown javelin wouldn't have a range/prof bonus or damage. Throwing a javelin would, somehow, magically, make it a different weapon that doesn't have an entry.
People claim, wrongly, the "specific trumps general" in a lot in cases where the rules work without needed "specific trumps general". If you can run the game with both the specific, and the general, at the same time, then "specific trumps general" doesn't trigger. In this case, there is no rule contradiction caused by a weapon having both the ranged and melee qualifiers at the same time, so "specific trumps general" is irrelevant. Note that "specific trumps general" also requires there to actually, you know, BE a specific rule.
Now, if there was an interaction between "counts as ranged when thrown" and "melee", then you would have something that could count as a contradiction: the thrown javelin would, under those circumstances, not have a weapon entry. At that point (and only at that point), you could try to invoke "specific trumps general" to fix the rules-break. However, given that there is no specific rule for what stats a non-melee javelin has, or specific rules for how thrown melee weapons get to keep their melee weapon stats despite not being melee weapons, the exercise would be somewhat futile.
A hypothetical case where "specific trumps general" would apply would be one where the rules for thrown weapons included "When thrown, melee weapons cease to be melee weapons. Use the melee weapon stats for their thrown properties". At that point you would have a contradiction between the general rule (melee weapons have stats on the melee tables, ranged weapons have stats on the ranged tables, thrown melee weapons, being ranged, would not have any stats) and the specific rule (thrown melee weapons get to keep their melee weapon stats). Sounds like a trivial example? Virtually all uses of "specific trumps general" are. That is the whole point. "Specific trumps general" sets how you handle rule contradictions by defining a priority scheme. It does not affect how you handle rule weirdness.