The problem is that if you remove either the i386 or x86_64 version of a package and try to reinstall it via rpm it tells you that some files in the already installed package conflict with the package you are trying to install, for example: Trying to install the X86_64 package for ImageMagick with the i386 version already installed reports says that some files in that package conflict with the i386 version already installed on the machine. This works in reverse too when trying to install the i386 version with the X86_64 version already installed.
This is expected behavior, you need to (re)install and upgrade multilib packages simultaneously (in the same transaction) if the packages have conflicting paths.