If you're using some hidden object to control the scrolling of the screen, maybe you can link the bot spawns to the proximity of the object. Sort of like,
If Bot is not within [Viewport distance] of Scroll Thing --> Destroy Bot
If Spawn Point is within [Viewport distance] of Scroll Thing --> Spawn bots/Recreate bots
This way the bots would be destroyed when the object pans away to another zone, and spawned and/or recreated when it come back.