Some parts of the Sierras have large gaps that can only be filled by generating terrain using a different format or DEM with a different date. This is an issue with the DEM itself. A tedious PIA, but you can get things back in order with your only loss being time. You can also try using the older USGS SRTM data...
1) Note the tiles where terrain is missing, the IDs for which will be displayed in the bottom of the RW editor window
2) Rename the route's Terrain folder to "x_Terrain" (or whatever)
3) Download the necessary DEM from the following FTP:
http://dds.cr.usgs.gov/srtm/version2_1/SRTM1 (I believe the area you need is in
Region_03)
4) Extract the downloaded zip files to the Railworks\DEM\SRTM folder
5) Rename each file with "00" (zero zero) on the end (N35W101.hgt becomes
N35W10100.hgt)
6) Import the terrain using the built-in importer in the RW world editor
7) Noting the names from
Step 1, remove all other files from the newly generated Terrain folder.
8) Rename the new Terrain folder to "Terrain_New"
9) Copy the folder x_Terrain and rename the new folder "Terrain" - x_Terrain will remain as a backup should something go wrong
10) Copy all files from Terrain_New to the newly copied Terrain folder over-writing the files. The ones being over-written
should be those listed in Step 1