This is actually a known bug with VAPI's dashboard when you clone a squad, it doesn't properly carry over the system prompts from the referenced assistants, leaving them blank.
Quick fix options:
Clone via API instead of the dashboard Use GET /assistant/{id} to pull each assistant's full config, then POST /assistant to recreate them, and finally POST /squad with the new IDs. This preserves everything including prompts.
Restore manually Since you already reverted, just make sure to back up your assistant prompts somewhere (Notion, a doc, etc.) before any future cloning.