Matt, searching quickly I can find no official body who is responsible for this route. 

https://www.cicloturismo.net/paneuropea-cycle-track/#:~:text=The%20Paneuropean%20Cycle%20Track%20is,to%20face%20short%20hill%20hills.

is the only source I have found. It's certainly not an EV route.

It's not 100% clear from your post so I may ramble.....

First of all, if you're expecting to put in Paris and Prague and expect CT to follow an "official" route then I'm afraid that's not how it works. It will choose the best route based on CT's own calculations (and possbily more up to date information han a static route). 

Secondly, the website is far superior for planning - especially multi-day journeys - than the app. 

If you have a gpx file of the route you wish to follow you can either import it, or better still, use the "trace feature" to create your own route on top of the original. Adding viapoints will allow you to drag the route to go where you want.

Some "official routes" are available to use/edit on CT, available here: https://cycle.travel/routes

I am not sure that the app maps the French part along the Marne Rhine Canal properly?

As regards this, this is probably the case that CT is preferring an alternative. In my experience, CT never fully follows an official route and also, in my experience, there are good reasons for that. 

No planner is infalible but neither is any "official route". I find it much more helpful to consider a route as nothing more than a suggestion, an outline. Where I currently reside any bike planner worth its salt will tell me I'm on the EV Atlantic coast route. I'm more than 350 km from the Atlantic! :-)

The picture below shoes bike routes marked on the OpenCycleMap in Germany & the Czech Repulbic. Loads of options! 

I think the ‘Pan’ you’re referring to is the Paneuropa-Radweg, which looks like it was established by a German district council who wanted closer co-operation with their Czech neighbours. It used to have its own website but that appears to be down: there’s this German Wikipedia article. 

I’m not sure whether the route itself is incomplete or it’s just incompletely mapped in OSM, but in either case it looks like you’d need to supplement the missing parts with your own (or c.t’s) interpolation.

thanks for getting back to me.

Kind rgards

Matt