Resource Points are generated at the start of the recruit step, not before. You lose all resource points when you leave the Recruit Step.
For the Darkoth example, if you use Darkoth's effect when you have 3 Resources, after using the effect, you will have 2 resources. During the next turn, during your Resource Step, you will put down a resource. At the start of the Recruit Step, the game will see you have 3 resources and will give you 3 Resource Points. You may recruit any amount of characters/equipment up to a total of 3 Resource Points. For Plot Twists and Locations, you may not play them if they have a threshold of 4 or higher.
KOing a resource in this game is generally a big deal if it is not mutual. You will essentially be a turn back compared to your opponent, so you need to consider if it is really worth it to do so at that moment.