I have scenery of Lyon St. Exupery France and it came with textures to add to the FS2004/texture folder, I was wondering if they would still work if I put them in the Lyon St. Exupery/texture folder instead.

I'm sure it would...The author probably said to put them in the main texture folder because they might be shared textures that other sceneries might use. And it might just cause duplication of the textures if you have them in sepparate folders. But personally I knida dislike dumping files in the main folders just because it is impossible to tell what they are or where they came from if you want to unistall them. I guess it comes down to tradeoffs. But the quick answer is that it should work within the Scenery's Texture subfolder.

I'm like you, I don't want to put these textures in the main texture folder because if I don't like the scenery it will be hard to find and delete all the texture files I put in the main texture folder for this scenery.Im going to do what you suggest and put them in the scenery texture folder and see if it works.