Generally, it was not a bad idea

. There is a reason why Bethesda releases the patches, although, they do tend to make a bit of a mess sometimes. Do you have the latest version of Wrye Bash? If so, I would recomend going to the http://www.gamesas.com/topic/1384740-rel-wrye-bash/and asking there. Also, there are mods that do not work with the new version and need to be updated. If you can post your mod list, we might be able to help.