Thank you! I've wondered that, can't wait to see what he answer is.
Egypt had a solar based-calendar, so (to a decent approximation) on every named date the sun would be in the same place in the sky.
So all that would be needed was for it be known that the sun shined straight down the well on (for instance) the 14th day of the 2nd Month of Growth (I had to look up the Egyptian calendar to get that date!), and Eratosthenes just needed to measure on that date.
You and I could sit at Christmas dinner, and conspire to measure the shadow of a 1metre pole at solar noon on Easter Sunday, at our respective locations.
We could then compare those measurements when we meet next Christmas.