sys-devel/flex does only install all files for the native ABI and only a limited set for all other ABIs. But in src_install it tries to rm "${ED}"/usr/share/doc/${PF}/COPYING for all ABIs. Since the file does not exist for none-default ABIs, this fails. Simple solution: Only rm this file for the native ABI.
This sounds like a portage-multilib bug, without any additional info.
This is an issue for any external tool that cross-compiles the package (like cross-toolchain, prefix and multilib-portage, check bug 711590 for ncurses as an example). I for myself and for multilib-portage can workaround this by setting COMPLETE_MULTILIB=yes in the environment. The easiest way to fix this for everyone (as COPYING should the the same for any target ABI) would be to use 'if multilib_is_native_abi; then rm "${ED}"/usr/share/doc/${PF}/COPYING || die ; fi' to only remove the file when it is actually installed.
multilib_src_install_all should only be invoked once, for the default ABI. The only way I can see a problem is if src_install is invoked more than once. That would not happen under normal circumstances. Please provide a build log demonstrating the problem.
