Hey there!
I consulted with a Development Support Specialist about this issue, and essentially what happens when you skip a section of the Workout is the program fills the skipped area in as null data or absence of data. It is up to the application that you are uploading to to be able to interpret this null data as non-riding time and ignore it, however, Strava does not seem to be doing that unfortunately 
Is skipping parts of your workout something you do frequently?
If so, it may be better for you to pick a different workout, or to edit the workout ahead of time using the Workout Creator to prevent this issue from recurring.
I’m sorry we don’t have a more elegant solution for you at this time.
Happy Training!