First of all, please note that when you activate the Fighter UCAV, you will receive bonuses only from those Skills which you assigned to the active Skill slots.
In the Fighter UCAV tab you have up to 6 unlockable slots, in each one of which you may select 1 Fighter UCAV Skill. Once you activate your Fighter UCAV, the selected Skills will start providing you with the appropriate bonuses.
Also, please note that percentage based Fighter UCAV Skills, that accelerate your Contract upgrades, building upgrades and troop training process, actually increase the upgrade/training speed, rather then cutting off certain percentage of time.
When you activate your Fighter UCAV with a unit training speed bonus applied, all your training queues remaning time will be recalculated with your new training speed taken into account.
For example, let's say it takes 2 hours to train 100 Riflemen, then your normall training speed is 50 Riflemen/hour. with the 20% Fighter UCAV bonus active, you training speed will increase to 60 Riflemen/hour, so with the Fighter UCAV bonus activated, it will take only 1 hour and 40 minutes to complete the same 100 Riflemen training.
On the other hand, if the Fighter UCAV bonus expires before the training queue is complete, the time needed to traing the remaining units, will be recalculated once again, with the decreased speed now taken into account.
The exactly same principle applies to the building upgrade process. While the Fighter UCAV bonus is active, you building will be upgraded at a higher speed, letting you complete certain % of the upgrade (let's say 70%) faster than you normally would, but once the bonus expires, the time needed to complete the remanining 30% of the upgrade will be recalculated once again.