When I titrated iodide with S2O3(2-) I used starch as an indicator, at equivalence the color changed to colorless. Then I left the solution aside after a while the blue color reappeared.

Iodide was probably oxidized by the oxygen in air to iodine. The only other explanation is that there is a trace of iodine that was bound in some precipitate or something like that -- when that iodine was released, it reacted with the starch. I'm not sure if I can think of any other explanation.

Or perhaps did some Iodine was on the inner wall of your flask, then it slowly came down, adding to the titrate more iodine, thus the blue colour reappeared.