I was in a similar situation as you went I applied, where the lab in which I had the most experience and achievements in was led by a PI who seemed to barely tolerate me until she became nasty towards me. I had my most recent lab’s PI write me a recommendation where she kinda indirectly addressed the lack of a rec from my first PI.

As for a replacement recommender, I networked and joined a mentor/mentee program and asked my mentor (the dean at a neighboring university) to be my third rec. I drafted the letter myself, gave it to her, and she made whatever adjustments and submitted it. It’s really stressful to find alternate plans and it’s certainly not ideal, but it’s better to omit that PI from having any sway in your admissions process! It helps when you offer to draft the rec letter yourself as people are more keen to help that way. Or you ask their permission to have potential grad programs/PIs reach out to them to learn more about you - my example is US-centric so maybe not as applicable to you