A little late here, but what you're referencing here are the Timeline Segments that I talk about in
this thread. You can go to the point in the video where you want to start displaying the full map, click Add, then change the Time dropdown to the first option, then change Active to Hidden. That would hide the whole map until it reaches the point in the video where you clicked the Add button. It would then display the entire map.
I don't think that's exactly what you're looking for though. It sounds like you're looking to only show a specific portion of the map from the data file. To do that, it's honestly probably easiest to manually manipulate the CSV file to remove the rows prior to what you want to display. You should be able to match up some sort of time column with a time in the video and delete the corresponding rows. If you want to keep other data like speed when deleting those rows, then it probably requires a different strategy (i.e. either adding or modifying a
GPS_Update column to indicate when you're actually getting new GPS data). Given that you're talking about hours here, that's probably on the order of tens of thousands or even millions of rows to delete though. Definitely possible, but might require a decent computer. Note that this may alter the size of the displayed map such that it requires manual resizing to get it to overlay on top of other maps nicely.
You could also try opening the config for the Input File and clicking the Trim button near the top right. I haven't ever actually used that, so I don't know if it would affect the track map itself. If it does, you could simply import your data file multiple times, and trim it accordingly for the segments that you care about.
I'm not currently aware of program that would smooth out or let you alter your GPS coordinates which would probably be the best solution for you.