Depends on if an infection vector can get in there without being neutralized before filling.
Even if you store them upside down in a clean, "sanitary" rack (e.g., dishwasher), I still would resanitize the opening before filling, just to be sure.
Some sanitizers keep working as long as the surface remains wet with it, such as Starsan. But leaving them overnight chances are the surfaces will dry up, and sanitation can be compromised.
Other sanitizers (such as Iodine based ones) work only for a limited timespan.
Regardless, if they're already clean, I still think (re-)sanitizing a few bottles at a time, right before filling them, is the safest option.
Don't forget to sanitize the caps!