Yes, you would have to use another counter to do this. Configure a simple Edge Count Task using the external encoder signal as the sample clock. The source of the edges should be one of the internal timebases. Since the counter would be synchronized to the other tasks, each sample of the edge count task would give a timestamp relative to the start of the acquisition (in terms of ticks of the known internal timebase).
Be aware that the counters do rollover once they reach their terminal count. On the 628x, the 32-bit counter would roll over just shy of 12 hours if counting the 100 kHz timebase (which gives a 10 us resolution of your timestamp).