Sound like when you patched, you did a replace. So the only thing in the folders are the patch files and everything else got removed. Some operating systems treat folders as files and just change them out. You may have to patch each folder individually if theres not a way to merge/overwrite existing files in folders
You can check if this is the case. In the RenderEffects folder, the MPL folder should have around 50 files and SPL 79 files. The patch only contains 3-4 files per folder so if thats all you have, that is what happened
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