If this happened after you updated the software or moved it to a different location, it is a result of a bug in Windows 11, which gets confused when an executable file is moved and fails to update the association. The workaround is to delete the existing registry keys so that Windows allows you to create a new association via the normal Windows methods. For the example of associating cif files with enCIFer the keys to delete are
Computer\HKEY_CLASSES_ROOT\.cif
Computer\HKEY_CURRENT_USER\Software\Classes\Applications\encifer.exe
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