Hi there,
Thanks for writing in! It depends where you did your modifications. The version of UberMenu included with the theme is an unmodified version of the plugin. So if you didn’t change the plugin files then you can update the plugin to new integrated one. If you want to keep the modifications, make sure to keep a backup of them (as I am not sure where you placed the codes). Also it’s always recommended to keep a backup of full site before proceeding to update.
Cheers!