Let us discuss Lain's power level. This obviously depends highly on the various interpretations of what or who Lain is. Some of these are:
>1
She is a piece of code in the implementation of the wired, an as such sees the communications of everyone and everything connected to the wired. She can freely alter these and thus has an impact on physical reality where it is connected to the wired.
>2
She is the consciousness of the planet, with every person being a neuron, connected by the internet (wired) at the speed of Schumann resonance (7-8 Hz iirc). This means she can control the planet the way humans can control their own body: through goals, choice of immediate action, but not very fine-grained (you can't decide to move just that one muscle at the power of 2.75 N, or to decide to kill some of your own cells). I'm not sure if she can see into the minds of her own neurons (people). Somehow she managed to make something forgotten on a town's level (perhaps not a person-by-person basis).
>...
>n
There exists an information layer, where Lain is a deity. There exists a physical layer as a shadow, a projection of this information layer, meaning that it's not physical signals (electrons traveling) etc that define the information they carry, but the information in the information layer is what defines or gives rise to physical reality. (Physical reality is a simulation running on no physical hardware.)
This last one is the most powerful interpretation one could give to Lain, but even then, I feel like her power level isn't that high. Please understand that when discussing high level superpowers, it's not the names, definitions, or interpretations of the definitions that matter, but the relations between such superpowers. With that in mind, let's take a look at this:
http://powerlisting.wikia.com/wiki/Special:Search?query=iwakura+lain
If you explore the network of powers on this site, you will see that the top of the hierarchy is
Omni-Creator, which means omnipotent in every verse (story, piece of literature, universe, multiverse, omniverse). The single entry below Omni-Creator is Omnipotent, which can do anything to anything regardless to anything, totally ignoring all logic, reason, or other powers and their restrictions. It can also not be given or taken by any power less than itself. Some powers are technically equal to Omnipotence, but are somewhat less; these are usually called Sub-Powers or Variations.
If we think of Lain, the best she can do (with some generosity on behalf of the interpreter), is omnipresence, omniscience and cyberpotence. The first two however is likely local to the wired (thus not real), or relies on the existence of an information layer (in which case Lain is just 'borrowing power' from the information layer). Cyberpotence could be an omnipotence variation, but only if the information layer theory is correct, in which case again Lain is relying on some kind of reality to get her power, thus it is not innate to herself.
With these in mind, we can see that an actually Omnipotent entity could do away with Lain's universe, Lain herself, even if Lain is given an opportunity to do anything she can to do away with this Omnipotent.
Before any reply, I'd like to remind you that when discussing high level superpowers, it's not the names, definitions, or interpretations of the definitions that matter, but the relations between such superpowers. This is because human language allows contradictions to exist between various powers, but a hierarchical network graph of these powers do not.