I reported this years ago when I noticed this bug with my forerunner 935, but now with my 965 it still isn’t solved (or is reintroduced)
I usually use garmin connect to sync routes. That works fine and I can see and use the routes on my watch.
I sometimes use garmin explorer to make new routes (and due to bad experiences in the past, expert these routes, import in garmin connect and then sync)
But I thought, let’s try to sync directly from garmin explorer to my watch.
Well, that doesn’t work. All existing routes are deleted from my watch, and I had to send just an other bug report to garmin.