A navigation system comprises a GNSS receiver that receives GNSS signals on multiple tracking channels, an INS that generates inertial data, and a processor. A micro jump detection and correction module comprises an oscillator micro jump detector that monitors estimates of C/N0 in all tracking channels, and detects a micro-jump event when there is an abrupt decrease of C/N0 in all tracking channels. An offsets module defines a plurality of carrier NCO command offsets to search over signal Dopplers in all available tracking channels after the micro jump event is detected, and sends the carrier NCO command offsets to the GNSS receiver to be added to nominal carrier NCO commands. The micro jump detector selects a tracking channel with the highest C/N0 after carrier NCO command offsets are added to nominal carrier NCO commands, computes corrections for clock error estimates, and sends the corrections for the clock error estimates to a GNSS/inertial Kalman filter.