I’m having the same problem. Only thing to add is that it is getting progressively worse! Started with two completed routes showing as incomplete on CA but now that has risen to seven! As a serial badge checker this irks me.
I even tried to ride one route again to see if CA “saw” it but no change. My only solution is not to look into CA route selector 
Same problem. CA 3.61.0. I cannot get badges in companion app even if i re-ride the routes (tried yesterday). Here are the routes:
Itza Party
Mayan 8
Mayan Mash
Radio Rendezvous
Three Sisters
Turf N Surf
City and the Sgurr
London 8
Triple Loops (London)
Achterbahn
In the grand scheme of things, this isn’t a big deal, but it would be nice if it worked.
Here’s what’s weird, if I add the ones to “my list” that it shows I don’t have a badge for, then I look at “my list”, it does show the badges. So it’s like “my list” knows, but the routes page doesn’t.
I agree it’s not really causing any issues with my enjoyment of Zwift. Just really weird.
I’m up to eight now: Itza Party, Mayan Mash, Mayan 8, Three Sisters, Turf and Surf, Triple Loops, City and Sgurr and Radio Rendevous. Looks like some common denominator here. I also see the same checked route when adding to the list so it’s obviously some kind of bug.
Same for me but only one route missing. I completed the Mayan Mash and it shows as completed in Zwift but shows as uncompleted in the Companion App.
I have badges for every route except a few of the most recent ones. Achterbahn, Big Foot Hills, Casse-Pattes, City and the Sgurr, Greatest London Loop, Jurassic Coast, Legends and Lava, London 8, Mighty Metropolitan, The Mega Pretzel, Three Sisters, Triple Loops, Turf N Surf, Volcano Circuit CCW, Volcano Flat, Wandering Flats are all marked as not completed in the Comparion app despite having truly completed them and receiving the badge. It seems many of the these routes are the same problematic ones others are listing.
@shooj to help the Zwift team fix the problem, I notice a few interesting things. When I add the these routes to “My List”, they do show with a green completion badge. When I try to re-ride these routes, they still do not show as completed. It seems the list keeps growing; routes are now marked as not completed that were marked as completed just a few weeks ago.
2 posts were merged into an existing topic: Known completed routes missing from Companion app [3.60]