When you recall a fleet, you're simply cancelling the mission it previously had. The time the fleet takes to come back to the planet you've launched it from will be equal to the time that has passed since the mission started.
ACS attack/defend, attack, colonization, deployment, harvesting and transport mission can only be recalled during the first half of its mission. For example, once a transport mission has delivered its resources to the other planet/moon it can no longer be recalled.
You will also lose any unused deuterium from the ships.