I have had this happen to routes of mine a few times.
The only way to get the route back is by having the exact removed wayspot restored. It also has to appear in Pokemon Go, so if some other wayspot popped up in that cell in the meantime, you’re out of luck.
One of the wayspots I got restored in this topic (Restoration request: Various painted power boxes by muugeherder) had a route of my making attached to it. The Pokestop had been gone from the game for a few months, but once it was restored, the route that was previously archived was also restored back to active duty.
