I have also lost one of my scavenger bots. I was playing co-op with a friend and picked up the chapter 5 bot during our first session. After he quit for the night i played awhile solo. The next time we played co-op i noticed my bot had vanished from existence. I was able to pick up and use the second bot from the planet, but my first one has never returned. I have even redone chapter 5 twice picking up the bot again, but never being able to return it to my inventory.
This seems to have been a long lasting bug with lots of people getting nailed by it. You'd think after a few years it would have been patched by now. Seems to happen on xbox also.
I was looking into save file editors to try and manually add it back to my inventory, but haven't found any info on a good/safe one to use.