Well the main idea behind the option design is so that the settings are passive, when you change options in one instance of FlashFXP opening the preferences in another seperate instance would now show those changed value. Call it what you want but this is how it was designed to work.
With your suggestion there is no way for the options to be passive. Changes made within one instance will not be updated in any other open instance and a restart would be required.
With most settings this passive design works well. However I agree there are some cases where this causes some adverse effects.
I'm not saying your way is right or wrong, better or worse. We just see things in two different ways.
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