How to reproduce:
1. Open the attached project
2. Copy the 001 - Bulbasaur folder under assets/crawl to somewhere else for reuse
3. Delete 001 - Bulbasaur folder and place there any other folder with some prefabs
4. Run the command in cmd "C:\Program Files\Unity 5.4.0p2\Editor\Unity.exe" -projectPath "C:\Project\DemoTest" -quit -batchmode -executeMethod Bui
ldAssetBundles_Batch.BuildAllModelst (make sure the path to unity.exe and to project is adjusted per your environment)
5. Delete the folder you placed in step 5, copy 001 - Bulbasaur and paste it back to assets/crawl
6. Repeat step 4 and check the Editor.log
-Notice some details Total compressed size 101.2 KB. Total uncompressed size 339.3 KB
7. Delete 001 - Bulbasaur folder again and copy the duplicated one back to crawl folder
8. Repeat step 4 and check the Editor.log
-Notice some details Total compressed size 27.2 KB. Total uncompressed size 58.3 KB

Workaround: replace different folder under crawl and run the command. And then come back to pokemon folder again.
User attached the Editor-xxx.log for comparison.

Reproducible: 5.3.6p3, 5.4.0p2, 5.5.0a6