The .gnd file has a central table with a maximum of 250 entries for ground texture KUIDs. Each terrain vertex (the 10 m grid) inside the .gnd file may have one or more ground texture attributes which reference the KUID in the ground texture table. Naturally, each ground texture KUID can and will be referenced more than once. Each instance of the texture has additional attributes: Scaling, rotation, opacity. That's part of the vertex data, not part of the ground texture KUID table which only defines the types.
Merging two equivalent source .gnd files will form a single new combined .gnd file (ignoring .obs, trk, .bmk in this statement) with a single new ground texture table of 250 entries maximum again.
So, let's assume you have 200 ground texture KUIDs in module 1 and 200 ground texture KUIDs in module 2 but only 100 of them are identical in both modules. You would end up with 300 textures in the merged file. As there is not enough room for that, 50 texture KUIDs will be discarded and their references removed.