Do you mean customization from the Customizer? That should be fine.
You can do the Manual X Update Via FTP guide provided here to make sure to keep your settings untouch and to save you from switching to default theme that might re-set your menus and sidebars.
You can follow that guide even though it is talking about x, just substitute x with pro and you can get the latest pro.zip from your dashboard here in APEX.
And since you're now using PRO please delete the X theme that is installed on your site, to avoid conflict.
Lastly, clear your caching plugins and browser's cache after re-installing.
Let us know how it goes,