You can use the batch mode. From Usage.txt:
Batch of files :
1) Create a batch file. It is an UTF-8 encoded text file of which each line specifies a file or directory to add or remove from the bundle file list.
Each line starts with + or -. Plus means that the directory or file should get added to the list, minus means that it should get removed.
To specify if it is a file or directory, it is followed by FILE or DIR. The file or directory path comes after a space character.
Each line can have a maximum of 510 bytes. If it is longer than that, the rest is cut off.
An example file could look like this :
+DIR C:\Program Files (x86)\Steam\steamapps\common\7 Days to Die\Data\Bundles
-FILE C:\Program Files (x86)\Steam\steamapps\common\7 Days to Die\Data\Bundles\TerrainTextures
First, all files in the Bundles folder are added to the list. After that, the TerrainTextures file gets removed.
The resulting list of files is then used to perform the batch export or import.
2) Launch AssetsBundleExtractor with a command line like this :
AssetsBundleExtractor -removetypetree batchexport <batch file path>
-removetypetree removes the TypeTree of the exported .assets file so it can be used with Grim's UAE Beta 3. If you don't want to do this, remove it from the parameters.
This exports all .assets files in the bundle files. If the bundle file path is "<directory>\<file name>.<extension>" or "<directory>\<file name>", the output file path is "<directory>\<file name>_<assets name in the bundle>.assets". As an example, the bundle file path could be "C:\folder\Bundle.unity3d" and the bundle file could contain a file named "CAB-1234". The output file would be "C:\folder\Bundle_CAB-1234.assets".
AssetsBundleExtractor batchimport <batch file path>
This imports all .assets files in the same path as they were previously exported into the asset bundles. If the bundle file path is "C:\folder\Bundle.unity3d" and it contains a file named "CAB-1234", the tool will look for "C:\folder\Bundle_CAB-1234.assets" and import it into the bundle file if it exists.