I'm trying to alter an Integrated Transport Network (ITN) to remove all of the roads that are within a flood zone (a separate shapefile).
The ITN Network Dataset I'm working with was created by Clipping the original feature classes from within the downloaded ITN .gdb and then rebuilding the Network Dataset so that it is restricted to the county boundary I'm working within. The rebuilt Network Dataset works fine for routing.
However, I need to remove roads that are within a flood zone so I can compare travel times. When I use the Erase tool to delete the parts of the individual feature classes of the clipped ITN network that are within the flood zone and then rebuild the Network Dataset from the new feature classes I get the following error when I try to run Closest Facility or Service Area routing:
Error: The network dataset has no edge elements. It may be unbuilt.

I made the Network Dataset exactly the same way that I made the clipped dataset, just using the new feature classes that had the flood zone roads erased. The elevation, turn, directions and so on settings are all the same and the Network itself looks fine (the correct bits have been erased).

Have I done something wrong? Is there a better way to remove the roads that are within the flood zone than using the Erase tool?
I followed @Mapperz's suggestion below to build the network dataset again and I end up with the same output (see below image) and get a long list of build warnings/errors:
SourceName: ITN_RoadLinks_CLIP_FLOOD_1, ObjectID: 1, Invalid hierarchical value.
SourceName: ITN_NetworkDataset_Junctions_CLIP_FLOOD_1, ObjectID: 36332, Standalone user-defined junction is detected.
SourceName: ITN_TurnRestrictions_CLIP_FLOOD_1, ObjectID: 1751, Cannot find edge element corresponding to turn identifier 1.
The original Network Dataset and the Clipped Network Dataset seem fine, with both reporting to be Built. But then when I use the Erase tool to create new feature classes and then create a new Network Dataset, it never builds and looks weird:
