You are way over thinking it.
Presuming the water in the bottle was properly clean, potable and microbiologically safe to begin with, and you're a normal healthy human, the water in the bottle will be OK virtually indefinitely. A few days of a backpacking trip? No question.
If you have a bunch of sticks, leaf matter, or bugs, etc in the water, you can sterilize it and drink it within a day or two just fine. But if you let it sit and stew you might develop a problem, but if a problem develops it will not mater whether you drank some of it or not first.
Disease causing organisms generally need to be present in their hosts to multiply, or you need to ingest a good number of their spores/cysts. Neither of those conditions are likely to occur in your situation and transform your water from safe to unsafe.