The only thing you can change with my tool is the reported distance (and that only works with FIT or TCX export; Strava will ALWAYS recalculate distance if you upload a GPX file from my tool to Strava).
If you don't want the distance between the two tracks recorded, upload TCX files and export TCX or FIT files with the "Use Embedded Distance" option selected. Alterntatively, you can have my tool calculate your distance, but check the "Ignore Big Gaps" option. With this feature, you will need to set a time and distance that is smaller than the gap in your two files.
When you select the "Ignore Big Gaps" option along with the "Calculate Distance" option, my tool will recalculate the distance in your file, but if there is a big gap (like a ferry ride or something where you had your GPS turned off, etc.)... then it will NOT Add in that distance (as long it is less than the time/distance cutoff you specified):
- This is where you can find the "Ignore Big Gaps" option.