We changed our project's dependencies to leverage pyproject.toml instead of the setup.py which caused the same issue where the Cython (.pyx) files were not recognized by PyCharm's editor, but everything was built correctly. Every import from a Cython file showed squiggly red lines.

After upgrading from PyCharm Community 2024.3 to PyCharm Professional 2024.3, the squiggly red lines disappeared and the Cython files seemed to integrate properly.