All of your above comments are cop-out comments. The game is designed to work with mods. There is an override folder. It's how the game was designed. If the company doesn't want to deal with people, they shouldn't be in business.
There is NO warning whatsoever. Just a huge button that says 'Apply Update', and no option to agree/not agree with regard to anything, let alone removal of extant content.

Not a cop-out, just the truth. There is nothing stopping you from remodding it, which doesn't take that long anyway.

Yes there is. On the downloader (or what ever you call it, the thing that checks for updates), it tells you that any mods will be overwritten or removed (or at least it did for 1.2, not entirely sure on 1.3)

There is no truth in your statement, only your view. No, there is not. There is just a large button, as I said. See attached image.

And when you click that button, you get a modal warning.

That warning should be written large on the launcher, not after the player hits 'Apply update'.

Oy.

Hey, Hickory! Move the damn override folder to "My Documents/Baldur's Gate Enhanced Edition/override". Problem solved, move on already.

Thanks for completely missing the point. Duh!

While I agree that removing mods and modded files during the patching process is required, I think that the current behaviour in the enhanced editions is a bit extreme.

Before patch 1.2, the patching process would simply remove files in the override folder and replace, where required, game resources such as dialog.tlk. This would still kill all mods and would require their reinstallation, but would leave untouched other innocuous files in the main game directory and subfolders (other than override).

Now the patching procedure will literally nuke the game folder deleting also, for example, innocent files like ReadMe.txt, so make sure to copy elsewhere, as backup, all the files in the main game folder that you want to preserve, before applying a patch.