What if starting combat DOESN'T involve a scene change?
That's why I brought it up

In that case, screen wipes are a common short-hand for "time has passed", so I would create a quick screen wipe as a transition out of combat. You can use the screen wipe to hide the enemy being moved back to the default position.
The way I create my screen wipes is just create a large black png (bonus points for adding a little bit of style: "tear" the edges, feather the edges, or tilt the edges). Do a "show picture", assign your black image outside the bounds of the screen, then use the move picture command to move the wipe to cover the whole screen. While the whole screen is covered, you can then do what you need to do (such as setting the enemy to a default location), then use move image again and have the wipe continue to wipe across the screen. Describing takes longer than it actually happens. I think my whole screen wipe takes 30 frames to complete, so it hardly slows down the player, and maybe you can consider the short slow down on the player as "punishment" for not fighting or being more aware of their surroundings.
edit:
Shower thought:
Reframe it. Using the above mentioned transition effect to represent time passing, don't call it "run". Call it "auto-resolve".
In this case, you would not set the enemy to a default location but instead just erase them as if they had won the battle. By auto-resolving you could make it so that the player loses a certain amount of health, such as 25% or 30%, gain marginal exp and gold (maybe like 1/10th the normal amount if they did the battle on their own). So long as players don't automatically restore to full health between each battle, this effectively makes running have pseudo "ammunition" pool, where that ammunition comes from your remaining health. If the player doesn't have enough health, then they can't auto-resolve, and so they need to make a choice if the cost to their health is worth auto-resolving.
I kind of like this idea and may potentially implement it into my own game...
Just be sure to include a tutorial box to explain to the player the cost of auto-resolving: why they might want to auto-resolve and why they might not want to auto-resolve.
1 more edit:
On the note of auto-resolve, you could also make auto-resolve require an item. If it's a tactics game, I can imagine something like the "Commander's Banner" or whatever. These items would be consumable. If the player has some in their inventory, they can auto-resolve. If they don't have any in their inventory, they cannot auto-resolve.