Sorry for the late response... been very busy recently...

The startup parameter should be something like
-uri <magnet>

The registry entry should be something like
[HKEY_CLASSES_ROOT\.magnet]
@="MagnetFile"
[HKEY_CLASSES_ROOT\MagnetFile\shell\open\command]
@="\"C:\\Programme\\Phex\\Phex.exe\" -uri \"%1\""

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