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In the morning on day 1 of my multi-day hike I opened up a one liter plastic bottle of water and drank half the contents. I stored the bottle in a loop on the outside of my pack and promptly forgot about it. A number of days later, sweating and thirsty I remembered the water bottle, but I worried that I might get an upset stomach if I drank the water.
Was I right to be worried?
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.
Did you backwash? Even if so several days.
I keep a jug by my bed that often goes more than a week.
If bottle was clear and hanging on your pack the the sun would kill bacteria.
wiki solar waster disinfection
Unless you have a weakened immune system, you're worrying too much. I've been in your situation several times, and never once gotten sick from my own water bottle.
If it didn't make you sick the first time you drank from it, it won't make you sick now.
If you're still worried about it nonetheless, or if you are immunosuppressed for some reason, I would suggest investing in a Steripen.
No, don't worry. At least in the US, and presumably a number of other countries, there are organizations that set the safety standards pretty high. As a result, IMHO, we've become much more suspicious of food that's not dangerous. You can backpack with unrefrigerated foods (like cheese and eggs) for a while, and they're still fine, but the safety folks would have to take deep breaths from a paper bag if they found out. ;) So...don't tell anyone, but I've left water in a bottle for months, drank it, and was fine. Now, I believe I have a pretty sturdy immune system, but I bet you're fine.
