Apparently multiple pack files can contain the same object hash. This error message will be shown:
Unhandled Exception: System.ArgumentException: An item with the same key has already been added. Key: 0b1bac8acae82a0d91133244c61400a3e409ce56 at System.Collections.Generic.Dictionary\2.TryInsert(TKey key, TValue value, InsertionBehavior behavior) at GitRewrite.IO.PackReader.BuildPackFileDictionary(IEnumerable1 packFiles) in C:\VCS\GitRewrite\GitRewrite\IO\PackReader.cs:line 87 at GitRewrite.Program.Main(String[] args) in C:\VCS\GitRewrite\GitRewrite\Program.cs:line 24

It is most likely not fixed by just ignoring already this error (not adding the file to the dictionary), as I think the diff restoring algorithm always operates on only one packfile at a time.

The workaround for this is running a git repack with the -a switch before running GitRewrite. Please see the documentation of git repack: https://git-scm.com/docs/git-repack