I remember something similar happening many many moons ago in a now defunct British regional airline.
Aircraft was to fly Gatwick to Blackpool on a night freight run, weather was miserable,heavy rain,pilots did walk around removed gear pins and found crosswind was out of limits so went back to the crew room to wait it out.When the wind fell within limits they returned to the aircraft but did not do another walk around because of heavy rain,and departed.
It was only after they got airborne and tried to retract the gear they found out that the ground crew had reinstalled the pins , but rather then return, they decided to continue to destination.
The incident only came to light when ops later on wanted to know why the flight took so long !!