Disclosed are methods for synchronizing the time basis of logged data between an implantable medical device such as an IPG and an external device. The IPG logs various operational parameters as data and associates the same with a possibly-inaccurate IPG time stamp and a sequence number. Periodically, the external device sends accurate true time data to the IPG, which, like the operational parameter data, is logged with an IPG time stamp and a next sequence number. The IPG then orders the data sequences and timing sequences by time stamp in a combined data log, and divides that data log into regions in accordance with reset conditions apparent in the time stamp data. Slopes indicative of the relation between true time and time stamps are calculated for various regions on an intra-region or inter-region basis, which then allows for true time estimates to be calculated for the data sequences, thus providing an accurate time basis for the logged data. The true time estimates for the data sequences may then be transmitted from the IPG to an external device for interpretation.