Matt,
In regards to the first option, are you saying that I basically must re-include my operational layers after going through that process? Also, what are the ways to clear the REST cache through the application builder?
In regards to the second, after doing so, the layers were completely removed from the layer list so that I couldn't toggle them on if need be. I basically just need them to be unchecked from the beginning, but still there if I need them. Is there a way around this if the first option does not work for me?
Thanks for your help,
Braden