If you have installed a version of mods that was made before the 4.09 patch, then it's natural that 4.09 won't install correctly on top of that.
The correct process each time is:
clean installation-->official update 4.09--->mods that work with 4.09
clean installation-->official update 4.10--->mods that work with 4.10
...and so on.
You will have to install official updates on a stock, unmodified version each time.
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