Let's say you have a tree like this:

+ SomeFolder
+- pyproject.toml
+- directory
 +- subdirectory
  +- file.py

With contents of the files:

• pyproject.toml

[tool.isort]
skip = [
    "directory/subdirectory"
]
filter_files = true

• directory/subdirectory/file.py

import os
import collections

When using a command isort directory\subdirectory\file.py, the file directory/subdirectory/file.py gets fixed by isort.

If you change directory/subdirectory in pyproject.toml to be just directory, isort does not touch the directory/subdirectory/file.py, but I was unable to get isort to ignore directory/subdirectory.

As a workaround, you can use skip_glob with directory/subdirectory/* pattern, but it does seem like a bug to me, considering that this work fine for top-level directories.