The obvious answer is to make sure that they fill the pipeline when it begins to empty or is getting close to being empty, right?  

Wrong.

If the pipeline is nearly empty today, your salespeople are feeling scared, stressed, discouraged and demotivated.  If awful is how your salespeople feel, then do you really believe that NOW is the ideal time to get them prospecting?  I understand how badly you need them to get the pipeline filled, but from their perspective, and in the state they are in, are they capable?  Will they do it?

If their pipeline runs dry and that isn't the time to ask them to fill it up, then when would be the right time?

You won't like this answer, but it's correct.

Have them fill the pipeline, or in this case, add to it, when their pipeline is already full.  That's when they feel the most motivated, excited, confident, positive, relaxed and successful.  That's when they should look for more opportunities.  That's when they will be most effective and successful.  And adding opportunities to the pipeline is what will prevent them from ever having an empty pipeline.

This works just like the saying, "If you want something done, give it to a busy person."