Update:
It seems as if at some point Simulink saved inconsistend data to the used Simulink DataDictonary for one/multiple stored DataTypes.
In contrast to Matlab/Simulink in the past, where everything could be fixed by just manually correcting the file in an text editor, this inconsistency cannot be fixed easily anymore, since the sldd file format, despite only beeing an archive with xml files, is not actually human readable and therefore not "human fixable".
My "solution" was to recreate the entire DataDictonary.
It is sad to see, that Mathworks seems to try more and more to prevent users from finding workarounds for the many issues Matlab/Simulink has.