It's odd that anyone is having missing textures since the paths back to the regular vanilla Lotus L-39 folder haven't changed. It should look like David's post above though in the texture.cfg file. Scratches head...
The paths were relative -- up one level and down again to a sibling subfolder -- but all within the Lotus L-39 folder. The new folder, Lotus L-39-civ, doesn't have the \texture or \texture.bump subfolders, so the old (relative) path directions couldn't find them.