The internal oscillator of the MachXO2 remains active to the user logic during transparent configuration. The clock provided by the internal oscillator to the fabric will not stop or be influenced while the oscillator is also being used internally for background configuration. Although only one internal oscillator is within the MachXO2 device, the user and configuration clocks are sourced from independent clock dividers and resources.
Please see Internal Oscillator(OSCH) section of the MachXO2 sysCLOCK PLL Design and Usage Guide for more details.