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Gentoo Live 32 to 64 migration as clean as possible:

This is my method - letting portage track every file and package except glibc and ld-linux.so.2 loader. System and all services can remain running. If this is done correctly only 2 reboots will be required.

make sure system is completely up to date and has been depcleaned, preserved-rebuilt and revdep-rebuild - to clean up old 32bit libraries else lots of work later
a full up to date backup of the system is a good idea and has saved me in the past.
make sure you have an *identically* up to date 64bit multilib profile VM to create binary packages on. Ensure CFLAGS is going to be identical, or compatible (“-mtune=generic -O2 -pipe” is safe). Make sure USE flags are the same between the systems as this makes live easier when doing emerge -k binarypackage on the other side. If changes are required to CFLAGS then emerge -e world.

Steps

mkdir /migration-backup
cp /etc/portage/make.conf /migration-backup/

building cross compiler

emerge crossdev -av

convert /etc/portage/package.* into directories

crossdev -S -s3 --target x86_64-pc-linux-gnu

compile x86_64 kernel with ia32 emulation (use CROSS_COMPILE= to add a prefix to toolchain commands), reboot into it

make CROSS_COMPILE=x86_64-pc-linux-gnu- -j5

Change CHOST to x86_64-pc-linux-gnu
copy lib and /usr/lib and /bin and /usr/bin and /sbin and /usr/sbin to /migration-backup
make /etc/env.d/99migration with LDPATH=/migration-backup/lib:/lib32:/lib64:/migration-backup/usr/lib:/usr/lib32:/usr/lib64

env-update
source /etc/profile
ldconfig

mkdir /lib32
mkdir /lib64
mkdir /usr/lib32
mkdir /usr/lib64

If applicable, dont use distcc till its remerged:

rm -Rf /usr/lib/distcc

back up these 32bit crossdev versions, they may be useful if something goes wrong (experience says it may!)

cp -ar /usr/x86_64-pc-linux-gnu /migration-backup/usr/

cp -ar /usr/include /migration-backup/usr

put -sandbox -usersandbox in features
add */* abi_x86_32 to package.use
most 32bit doesnt get built on stable unless u do this:

# cat /etc/portage/profile/use.mask
-abi_x86_32

change make.profile symlink to point to a multilib amd64 profile

on donor pc or VM:

quickpkg glibc gcc zlib ncurses gmp mpfr util-linux acl attr sandbox coreutils procps binutils libcap mpc cracklib flex =db-5* glib pam pambase =python-3.6* bash readline findutils install-xattr bzip2 tar xz-utils make grep patch gawk sed libpcre dev-libs/libffi gettext libxml2

on source VM, scp -r /var/cache/binpkgs to target PC

for this lib / lib64 link ↔ switcheroo
* make sure busybox is functional. run this from busybox
* have a few shells open, in case you break the one you're working from

mv /lib oldlib
ln -s lib64 lib
cd /usr
mv lib to oldlib
ln -s lib64 /lib

this will get overwritten by emerge at the appropriate time, but lets the 32bit loader continue to work for now

cp migration-backup/lib/ld-linux.so.2 /lib

/usr/lib symlink creation will break python. The following will not create orphans as the files are in exactly the same location from portage's point of view.

cd /usr/oldlib
mv python-exec python3.6 libpython* portage gcc ../lib64
cp -r gentoo /lib

use quickpkg on source VM to grab and then PATH=“/migration-backup/bin:/migration-backup/usr/bin:/migration-backup/sbin:/migration-backup/usr/sbin:${PATH}” emerge -1kav to deploy initial binary packages donated from prebuilt VM from /usr/portage/packages or /var/cache/binpkgs. Of these, glibc needs to come first, then everything else will come good. In the process of deploying glibc, /lib needs to be a symlink to /lib64 which will break 32bit programs. see ld-linux.so.2 trick above. ldconfig is your friend here with the above 99migration env file.

backup these: /etc/env.d/99glibc /etc/gai.conf /etc/host.conf /etc/locale.gen /etc/nsswitch.conf /etc/rpc
to get 64bit loader and glibc working, extract glibc tbz2 binary package directly into root of filesystem. subsequent remerge will track the files correctly later.
restore etc files from above backup

remove crossdev packages (and crossdev) and check gcc sanity

emerge --unmerge cross-x86_64-pc-linux-gnu/* crossdev -av
ldconfig

fix 32bit toolchain and python in wrong directory by running:

PKGDIR=/var/cache/binpkgs emerge -1kav sys-devel/gcc mpfr mpc binutils 
gcc-config 1
binutils-config 1
. /etc/profile

Example final binary emerge. Note obvious package version changes required based on source VM:

PKGDIR=/var/cache/binpkgs USE="fix any differences" emerge -1kav =zlib-1.2.11-r2  =ncurses-6.2-r1  =gmp-6.2.0-r1 =util-linux-2.35.1-r2  =acl-2.2.53  =attr-2.4.48-r3  =sandbox-2.13  =coreutils-8.31-r1  =procps-3.3.15-r1  =libcap-2.26-r2  =cracklib-2.9.7  =flex-2.6.4-r1  =db-5.3.28-r2  =glib-2.62.6  =pam-1.3.1-r2  =pambase-20190402  =python-3.6.10-r2 =bash-5.0_p17  =readline-8.0_p4  =findutils-4.7.0  =install-xattr-0.5  =bzip2-1.0.6-r11  =tar-1.32  =xz-utils-5.2.4-r2  =make-4.2.1-r4  =grep-3.3-r1  =patch-2.7.6-r4  =gawk-5.0.1  =sed-4.7  =libpcre-8.43 =dev-libs/libffi-3.3-r1 =gettext-0.20.1 =libxml2-2.9.9-r3

Finally now that theres a working coreutils etc, binary glibc package can overwrite the manual tar version we extracted in a previous step.

PKGDIR=/var/cache/binpkgs emerge -1kav glibc

Double check /etc/nsswitch.conf and other files backed up above, this may have overwritten them again.

  
mv /migration-backup/lib/modules /lib64

Emerging gcc needs to be done now, but also acts as a sanity check to see what we've missed. Repeat the quickpkg / emerge -1k steps for missing things

emerge gcc -1av

leave /etc/env.d/99migration in place at least until libraries in /lib32 are populated

@system rebuild - adjust USE as needed

FEATURES="-sandbox -usersandbox" USE="-X -gtk -qt5 -introspection -cairo -gpm -consolekit -policykit -net -ipv6 -spell -sqlite -nls -berkdb -gdbm -openssl" emerge -1eav @system

work through any problems caused by emerge ordering above. If a dependancy problem proves too hard to solve, cheat by grabbing a binary package from the donor VM prepared earier. The subsequent @world emerge will take over the package later.
/etc/env.d/99migration can now be removed. env-update, source /etc/profile, ldconfig

remove -sandbox and -usersandbox from features
check for i686 compiler orphans with: qfile -o /usr/bin/i686-pc-linux-gnu-*

emerge -eav –keep-going @world

take note of failed, packages - these are usually caused by ordering/dependancy so a subsequent emerge run of the failed list will work. If not, work through the issues.

Things to do later

uncomment LINGUAS from make.conf
take out /etc/env.d/99migration
remove /migration-backup
erase /usr/portage/packages (whole dir)
remove abi_x86_32 from package.use and profiles/use.mask, then emerge –newuse
clean up /lib.old and /usr/lib.old

check for orphans in /usr/lib and all the other places. (bin sbin /usr/bin /usr/sbin). For finding orphan files after migration in /lib32, /usr/lib32, /usr/lib64

cd /lib32 ; find  -xdev -type f -exec qfile -o {} + |less

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