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I wanted to know the limitations of Visual editor in Optimizely? I am running a A/B test and wanted to make a few visual changes in my app. Can I make these changes when my app is live ?

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The only limitation I could think of would be... it wont execute javascript for you. And the order of execution that it would be executed last, after the custom JS/CSS.

Yes you can make changes when your website is live, so long as you don't publish it wont get reflected on your website. Utilize the preview mode to making as many changes as you want.