I have MDT v3.0.2. I deleted ALL the old routes from Season 3 using the SHIFT+CLICK delete button.
I created a few routes for AD, SoB, ToS and UR and after logging out of the game and back in I found all these routes were gone. After a little debug I was able to isolate how to recreate the problem.

If you bring up the "Default" route and make changes to it and then "Rename" to save it that renamed route will get deleted after logout/login.

However, if you click the "NEW" button and create your route that way it persists through logout/login. You can also rename routes created with the "NEW" button and they persist as expected through logout/login.