Hey, thanks for the report. This is a known issue with Gemini models in Plan mode. They create new plan files instead of modifying the existing one.
Try this workaround for now:
- Switch to Claude 4.5 Sonnet or GPT-5 for Plan mode. They work reliably and update the existing plan.
- Or you can explicitly ask Gemini to edit the previous plan (as @liquefy suggested), although this isn’t guaranteed.
The team is already working on fixing this model-specific behavior.
Related report: Plan mode allows editing files still (Gemini 3 Pro especially bad for this)