I also somehow came into possession of the :11 version as well and deleted it from my game causing a lot of industries to break across multiple routes. I also attempted to replace them like you did by changing the kuids in the route configs. What I found worked was setting the route's config...
The only routes I have experienced this on so far are Hawaii Railway from CPS and Gila Railway from NARM. The former upsets me the most because I used it quite a bit for screenshots and it was perfectly okay prior to SP6. Gila did have draw issues during SP5+HF1, but that could be resolve by...