Did it actually conflict though? The last line of the last episode implies that it is September 2nd (mentioning Liberal Arts City tomorrow)... considering the stills included Accel+LO and Touma in class, I am guessing it sailed right past Volume 5 (the last day of summer break). It would have been better if Unabara were shown or even a passing mention of helping Touma with his homework, but I don't see how it directly contradicts the existing timeline. Mikoto just needed an hour or two to herself on August 31st.
(Note: I got my timeline info from the "A certain unified calendar" graphic available on Baka Tsuki's site... I would say that format is the best way to keep all the stuff straight without having to read through walls of text).
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