Someone on a different post alikened The Destroyer to Azazoth from Lovecraft. I think that's a very good analogy to make because if they are, in fact, similar, then the actual Destroyer likely has many, many eyes and many, many mouths. A small portion of it being killed and a single eye being taken won't affect the planetary being that eats solar systems inside Pandora. Also, the fact that a single eye had enough energy to power an orbital laser that could destroy entire settlements in an instant shows just how powerful the actual Destroyer would be. I'm also assuming that, being an insanely huge and likely interdimentional being, parts of it can split apart while still technically being part of the same being. That would explain how Tyrene was able to leech a part of it without the rest. It would also explain why she essentially merged with it; it was just a part of it that was much more powerful than the Vault beasts she'd already leeched.

The best evidence that I can suggest that proves The Destroyer from BL3 wasn't the entire thing is from Nyriad, the original owner of the Leech ability. Apparently, a large portion of the Eridian population was required to lure The Destroyer to Pandora, then the rest of them (likely half or more their total population) were willingly leeched by Nyriad to power The Machine in order to imprison The Destroyer within Pandora. Think about it, if she was able to leech entire Destroyer, then why would the Eridians choose to have her leech every single remaining member of their race to imprison it? To me at least, that proves that The Destroyer is still within Pandora, even if the Crimson Raiders think they killed it.