This bug has been fixed in Release 2006a (R2006a). For previous product releases, read below for any possible workarounds:
Documentation on how to detach a configuration set from a model from the command line is missing in Simulink 6.0 (R14). Here is additional information on how to do this:
You can use the DETACHCONFIGSET command for this purpose. The following example illustrates the use of this function.
vdp
x = Simulink.ConfigSet;
x.Name = 'new config';
attachConfigSet('vdp',x);
detachConfigSet('vdp','new config');
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