Dragon-Soul: Yes, you could do that. On any given turn you get an action, an item interaction and possibly a bonus action or reaction. Those last two need to have something allows you to get them. You also get to move.
In this case I would consider throwing your rapier to be an item interaction. This means you would still have your main action if there was something else you wanted to do. FYI - throwing the rapier would be your action if you were trying to hit something with it (The sort off thing that needed a to-hit roll.) because it would be an attack. But, just lobbing it forward? That is just an item interaction. Calling it back to you using the bond is a bonus action. So item interaction it out and then bonus action it back. That works perfectly. And as I said, you'd still have your movement and an action left if you want them.
Most of what you can see right now is just dust, but yes, there are some boulders forward of you that you could easily duck behind. And, as you seem to understand, you really don't know where you are throwing the rapier because of the dust. Just forward somewhere. But that works.