Adding another voice to this.
I have narrowed it down to this;
If you play the prologue chapter with a bot that is out scavenging then you will lose it.
For me I had been playing NG+ looking for an artifact on chapter 4 on easy. Saved with a bot out scavenging. Decided to start an impossible difficulty run through. When Chapter 1 started my bot was missing.
The same thing happened when I joined a a new coop game. I had been messing about in the weapon crafting arena and had dropped a bot. Then accepted an invite to join a coop game. By the time I was back at chapter one I was left with only one bot left.
As I have (stupidly it seems) paid for the Bot packs - because I was using them a lot - I fell rather agreived that I now have no option but to start completely from scratch in order to get my bots back.
Given how long the game has been out and this bug being reported I don't hold out much hope for it being fixed. I am not really in the mood to play through everything again so that I can have my bots back before getting the new story DLC so I guess the game goes to the trade in now. Shame.