It’s difficult to answer your question because I can’t determine whether your priorities are to keep the time in HH:MM:SS.FFF format or to display all the samples.
One possibility is for you to keep all the original sampling times and simply label your time axis every millisecond. (That would be my approach.) This might require a visit to the realm of handle graphics to set the 'XTick' values to be only where you want them. You will likely need to use the datetick function to label your time axis in any event.
Another possibility is to average them over every millisecond and simply display them every millisecond. (That would not be my approach if I went through the trouble to sample them every microsecond.)
Plotting them with different start times would be relatively easy, since the plot function would take care of that automatically. I don’t see a need to actually label the start times on your time (probably x) axis though, unless that is an important parameter.