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If the option, which according to the logic should be disabled, is currently selected by the user, the module will automatically select the first possible entry, provided that the configurable option mandatorily requires a value.
Note that, except for the Yes/No type, each configurable option type requires a value. So it is technically not possible to remove all values, because WHMCS expects a selection. If you don't want to do this, we recommend adding a new configurable option selection with the value "None" or similar.
It is also important to understand that the module does not check if the logic you created is in conflict with another logic you created. For example, if logic A removes values that are added by logic B, this will cause a conflict. Because of the effort involved in such a check, we require (at least for the moment) that the rules be added thoughtfully by the WHMCS administrator.