Hmmm... this is why you never overwrite the default files...
My advice is to move all your mods to their own mod folders, then re-install (without uninstalling first) the game from the CD. Then patch it. Then use the mod-picker to pick your mods, instead of overwriting the default files.
you should be okay installing the patch and then re-installing proportions back to wherever it is now, except that proportions isn't yet Patch2 compatible. Assuming that the new patch is incompatible with old mods, that is.