I believe you accidentally flipped the inversion state for TalonFXs when moving to Phoenix 6 2025.
Here's my TalonFX in Tuner X with my drive inverted set to true in the json file.

Here you set the TalonFX to be CounterClockwise_Positive if it should be inverted but I believe it should be the other way around and that CounterClockwise_Positive is the default.
This can be further confirmed by the api for TalonFX.setInverted which sets the inversion state to Clockwise_Positive if the TalonFX should be inverted.

When moving from 2024 to 2025 I had to invert all my drive motors (TalonFX) which struck me as weird.