That is interesting. While I am not sure of the answer, I do have a few suggestions.
1. In the LumenRT Exporter, their is a script input option at the bottom of the dialogue box. Write a script to reclassify the terrain values from 0 to 65535. This will prevent that from messing up the terrain in CE because it takes place during export.
2. Reclassify a copy of the terrain (normalize 0 to 65535) in ArcGIS before you import it into City Engine. Use this as your terrain before you export....While this may look ridiculous in CE viewport....it might give you the result you need in LumenRT because currently you are getting "flat" terrain with a small range of values...so a very large range could result in the actual terrain.
3. Get E-On LumenRT on the phone! The reason I say this is because, while the LumenRT software is awesome for scene creation, it is very buggy. I kept losing animations and textures in my scenes after hours of work....I emailed them files and never heard back. I kept pushing until a support tech called me and they talked me through the problem...after waiting almost 2 months.
Good luck .... I will be interested to know how this works out.