Flattening hidden layers

I found a tutorial on ( www.comeandphotoshop.com/animated-neon-sign/ ) and followed it up to the point of animation. The effect worked fine but it involved stroking outlines then hidding the layer and creating a new layer and adding the effects to the new layer. So far so good everything looks great. Problem is when I flatten the layer to send out to web as a jpeg I get a box that says flattening will disguard all hidden layers. This looses some of the effect. Can you get past the deleation of hidden layers or is there another way to keep all effects? I need to save my hidden layers but can't keep them visible or once again it ruins the effect.
Any help would be appreciated,
Thanks
Chuck

Again.
When you flatten, ALL layers are discarded. Flattened images don't have Layers, by definition. Any layer that had the visibility turned off will have no effect on the way the image looks whether it's flattened or not.
Are you looking at this at 100%? Something else must be going on.
Maybe what you mean by "turned off" is different than what I think. Are you clicking on the eyeball? Are you setting the Fill Opacity to zero perhaps (which is what I would do)?

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