I'm answering here instead of scriptorium thread about patching over modded files:
patch will probably overwrite some of modded files, trying to patch over mod is likely to leave you with nothing at all working! Make copies of all files you've modded and save somewhere separate, uninstall and re-install if you don't have a spare clean copy of game and then apply patch.
If you have space make a copy of the clean unpatched version before patching other one. Then compare files before and after patch, if they haven't changed you should be able to re-introduce your modded version. You could always try using the changed files to make mod-folder I suppose just in case it works...
For ones where vanilla file is changed by patch you'll need to go through them individually and make same changes to patched version you did before, or identify what changed in patch and make those changes to modded version if that is quicker...
its liable to be a bit messy I'm afraid - there is a thread in here somewhere (hopefully in answers) about converting mod between patches.
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