I have looked at your i2c trace, and the reason why you are seeing num_bsec_inputs as 0, is because the first byte read back from 0x1d (based on your I2C trace) is 0 and that means (bit 7: new_data_0) is also 0, so the statement if (data.status & BME680_NEW_DATA_MSK) yields false.
It would be helpful if you share more I2C trace data (preferrably from the start of the device to a point where 0x1d reads back, and preferrably the original trace format (assuming it's logicdata extension for easier analysis). I can look into it when you share the trace data.
P.S. it would be appreciated if you could also compress the trace data (because the original format might be much bigger in size)