Hi Fredo, hi Erik!
Thank you for your replies!
Now, the project is finalized. For rerecording, we transfered from Nuendo to Protools and repaired all fadecurves there, bit by bit, which were audible. At the end, it was not such an effort.
Another strange thing we found out - maybe interesting for further Nuendo-Protools transfers: very small edits (like smacks cleaned with Izotope in Nuendo) were not been transfered by AAF. In Protools we found some very small holes there on these places which produced clicks.
In conclusion, its better to keep working in the same DAW. 
Stefan