Updated my Windows OS, will my Skyrim mods still work?

[lnx465]

Like the title said. Well, I updated my Windows 7 from 32bit to 64bit. The problem is i want to know whether my mods will still work when I play the game or no? Because I think the Windows doesn't detect all of my games that i installed before I updated it. I installed Nexus Mod Manager and the mod manager doesn't detect any mods (I scanned the game directory) but when I use the game launcher and go to data files, I can see all the .esp files and other stuffs.

So, like I asked, will the mods still work even though I upgraded my OS and the Nexus Mod Manager doesn't detect mods that I've installed before I upgraded my Windows?

Sorry if you don't get my question or whatever, my english isn't very good.