Time is tracked in a downhole tool to indicate whether timestamps associated with data samples or events in a log indicate either real time or a duration of time since a certain reset, and to indicate whether the timestamps have been synchronized with a master clock in the tool. The log also records the time and offset of each synchronization event. A computer processes the log to convert all of the timestamps to real-time values and to indicate timestamps that have been estimated and timestamps that were never synchronized to a master clock in the tool. The computer determines an associated uncertainty for each of the estimated timestamps.