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Well, basically some sys attributes (including meta_path) are cleaned during shutdown, so if some code executes afterwards and tries to import something, importlib will complain that meta_path is empty.
Unless the warning is genuinely useful, I would suggest simply removing it.
Printing warnings during import can also degenerate into an infinite recursion, if printing the warning needs to import a module, for example:
./python -Wa -c "import sys; sys.meta_path = None; import logging"