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Showing content from https://github.com/pandas-dev/pandas/issues/11599 below:

BUG in remove_unused_categories with NaNs in values · Issue #11599 · pandas-dev/pandas · GitHub

removed_unused_categories gives a wrong result when there is a NaN in the values:

>>> s = pd.Series(["A", "B", pd.np.nan]).astype("category")
>>> s.cat.remove_unused_categories()
0      A
1      B
2    NaN
dtype: category
Categories (3, object): [B, A, B]

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