I recently picked up Descent 2E and am having a lot of fun with it (yay!). So far, I only have one question when it comes to remaining search tokens on the field once the victory conditions are met. A couple of the players believe that picking up the search tokens after the fact would be reasonable. They defeated the bad guys and now have all the time in the world to conduct searches. This means that it effectively gives them extra gold at the end to spend in town. The part I'm concerned about is that the players will always hold the field after the encounter, thereby ensuring they always get the money. It concerns me in balancing for the OL player in the long run if the heroes don't need to go after the search tokens in an encounter if they will pick them up at the end anyway.

This is pretty clear cut. Once the heroes or OL reach the goal the encounter is over immediately. There's no "holding the field" or any other thematic explanations. Letting your heroes grab all the left over tokens will seriously affect the balance of the game and end up with your heroes getting pretty powerful rather quickly.

This game is NOT D&D. Think of it more like a video game. When you beat the level you don't get to go back for all the coins.

If the heroes don't search before the goal is reached they do not get the left over tokens. This was done intentionally to make searching a complication you have to weigh against completing the goal of the encounter.

They defeated the bad guys and now have all the time in the world to conduct searches.

The heroes DO NOT have all the time in the world to conduct searches. There's an evil Overlord out there threatening to conquer the world, man! He's not going to stand around and wait for the heroes to finish whacking the bushes in the forest. For this reason, the heroes must hurry along to their next encounter/quest in order to stop the Overlord before it's too late.

If the Heroes try to argue that they should be allowed to do that, the OL should argue that after the first encounter, if the OL wins, they should be allowed to draw the entire Overlord Deck into their hand, because the OL could have just sat and waited for X number of turns to do so if it didn't end immediately.

Obviously that's absurd, but hopefully it would be enough to convince the heroes of the potential balance issues that getting all the search tokens for free would provide, too.

If the Heroes try to argue that they should be allowed to do that, the OL should argue that after the first encounter, if the OL wins, they should be allowed to draw the entire Overlord Deck into their hand, because the OL could have just sat and waited for X number of turns to do so if it didn't end immediately.

Obviously that's absurd, but hopefully it would be enough to convince the heroes of the potential balance issues that getting all the search tokens for free would provide, too.

Yup, and also what Steve-O said. The encounter ends exactly when the quest guide says it does- that means if the heroes put off victory for one more turn (and allow the OL the opportunity to pull a surprise victory or get a useful card for encounter 2) for the sake of some gold, that's a risk they need to consider.