YAGSL factory-resets the IMU at code startup:
https://github.com/BroncBotz3481/YAGSL/blob/4016ee219003baabd6fe0ff481af86314ded9c42/swervelib/SwerveDrive.java#L281
For a Pigeon 2, this involves creating a new configuration object:
https://github.com/BroncBotz3481/YAGSL/blob/4016ee219003baabd6fe0ff481af86314ded9c42/swervelib/imu/Pigeon2Swerve.java#L92-L104
This configuration object includes the default values for all in-flash settings of the IMU, including zeroing the mount calibration.
YAGSL should not destroy the calibration like this, or at least provide the user an opportunity to disable the reset. This would allow teams with IMUs mounted unconventionally to still take advantage of this important feature.