As written, the text of Overhand Chop says only to add twice your Strength bonus to the damage roll—it says nothing about any other bonus based on Strength that is also added to that roll. So both bonuses are on there; you have not substituted one bonus for another.
So does that mean you get 3½×Str on your damage roll with Overhand Chop? Only if the two stack—if the two overlap, then instead you have to just choose the larger bonus, which will be 2×Str. The real question, then, is whether or not Overhand Chop’s bonus stacks with the usual bonus.
And the answer to that is no, at least according to the FAQ:
Do ability modifiers from the same ability stack? For instance, can you add the same ability bonus on the same roll twice using two different effects that each add that same ability modifier?
No. An ability bonus, such as “Strength bonus,” is considered to be the same source for the purpose of bonuses from the same source not stacking. However, you can still add, for instance “a deflection bonus equal to your Charisma modifier” and your Charisma modifier. For this purpose, however, the paladin's untyped “bonus equal to her Charisma bonus (if any) on all saving throws” from divine grace is considered to be the same as “Charisma bonus (if any),” and the same would be true for any other untyped “bonus equal to her [ability score] bonus” constructions.
Note that, despite the phrasing that pretends things were always this way, this is an errata that fundamentally changes the way ability bonuses behave; prior to this FAQ entry, they would have stacked, RAW. That was almost certainly an oversight—Overhand Chop should have had an errata saying it replaced the existing bonus—and in most cases, this change is probably for the best. But it does have some weird effects on the rules, where suddenly a “deflection bonus equal to your Charisma modifier” is vastly more valuable than just adding Charisma to AC directly, which wasn’t the case for a long time and therefore wasn’t accounted for by designers’ decisions. I don’t actually recommend ignoring it—ability bonus stacking is an extremely potent approach to extreme power in Pathfinder and it’s not a bad idea to throw a wrench in the gears—but it’s worth being aware of the history and maybe reconsidering some corner cases in light of it.
But anyway, it does handle the Overhand Chop situation—the bonuses don’t stack, so you just get 2×Str to damage, not 3½×Str.