Roger, I've done what you want to do.
First open REX and go to Configuration Manager and restore your backup. This will return all textures to default.
Then go to options tab and tick the textures you want REX to install. Make sure you leave "Water Animation" unticked.
Finally go to "Textures" tab, select the textures you want to install on the various themes (sky, clouds, runway etc) and click install. REX will install only the textures that you have ticked in the options tab.
Hope it helps.