If you just remove the 74LVC1G125, then only REST and INT are affected.
The gyro sensor inside BNO055 are powered on by 3.3V on the schematic, if both two are preperly powered, the gyro sensor should work fine.
From your description, the gyro are always output 0, can you try to do the self test on BNO055 then post the result here?
one more question: which virtual sensor are you enabled now?
I think a easy way is to power off then re-power on the boards to get BNO055 be HW reset.
You can buy BNO055 from Digikey and replace it easily.
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