If you delete an IPF, next time you start the game it'll redownload that file
To apply the patch, use IPFUnpacker to decrypt the IPF
To make this easy, make a couple of text files, edit them and have one be
ipf_unpack.exe %1 decrypt
and the other
ipf_unpack.exe %1 encrypt
and then rename them something recognizable and make the extension .bat, like New text document.txt into Decrypt.bat
That way, you can just drag-drop the IPF file onto either Decrypt.bat or Encrypt.bat and it'll do the work then and there
After you've decrypted the IPF, open it up in IPF Suite, and replace or add(Add container, and then drag-drop the subfolders into it if you want to save some time) the files, close and then Encrypt the file again and you should be good to go