I have a leak where the top part of the flashing has pulled away from the chimney. What do I do?

I have applied polyurethane caulk in the gap but the water is still coming in. I applied the caulk when it was below 40 degrees because it is winter. The caulk has solidified. Question - will reapplying the caulk when it is warmer outside then make the caulk able to keep the water out?