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In a GNSS software receiver, blocks of digitized intermediate-frequency (IF) data are prepared at the front end and sent to the processing unit for signal acquisition, tracking, demodulation, and position fix. A problem that is observed in practice when the GNSS software module is co-located with a mobile phone device is that the digitized IF data are subject to data intermittency. The intermittency results from the use of mobile phone when the GNSS signals are being received or the execution of higher priority routine in the host computer. An improper buffering scheme at the front end may also lead to such phenomena. Such data intermittency leads to burst-type errors (rather than bit-type errors) on the data to be processed, posing a challenge for the tracking of the GNSS signals. Indeed, if not properly handled, a typical tracking algorithm is not able to accommodate such a large data gap. In the paper, a decision-aided tracking algorithm is developed for a seamless tracking of codes and phases. The effects of data intermittency on code and phase tracking are analyzed. To accounting for the effect without going through the reacquisition process, a detector based on signal power and continuity is then implemented to facilitate decision making. It is shown, through the processing of field gathered data, that the proposed algorithm can indeed be able to continuously track codes and phases in the presence of data intermittency.