biocyberman

This is working: 
1. Downloaded the latest stage3 file of the same characteristics as the stage3 I used to install funtoo. 
2. Create a dir: /root/2018stage3
3. Cd to the dir: cd /root/2018stag3/ and save the latest stage3 there. 
4. Untar: tar xpf lateststage3.tag.xz. Waring for future readers: Untar the stage3 directly to root file system cause you to lose all customized files  in /etc (including passwd, group) and also list of installed packages. Be careful not to make this mistake. 
5. Follow the "Chroot into Funtoo" section in this guide: https://www.funtoo.org/Install
Now I have a working basic chroot environment similar to my Funtoo . I can use this to mimic the broken Funtoo and create compatible packages for it.  I am now following the upgrade process following this guide: 
 
After that I will create binary package to install on the broken system. It's a long workaround but still faster than reinstalling from scratch.

Found it!
The trick is "# emerge -auDN --newrepo @world". The '--newrepo' option is crucial.
Update 19 Oct 2017:
The command above works for more than 1000 packages I have installed, except the qt* packages. For these stubborn qt* packages I had to do the following:
emerge -Cav "dev-qt/qt*" * This action can remove important packages! In order to be safer, use * `emerge -pv --depclean <atom>` to check for reverse dependencies before * removing packages. >>> These are the packages that would be unmerged: dev-qt/qtsql selected: 5.9.2 protected: none omitted: none dev-qt/qtx11extras selected: 5.7.1 protected: none omitted: none ... truncated for clarity ... dev-qt/qtprintsupport selected: 5.7.1 protected: none omitted: none All selected packages: =dev-qt/qtwidgets-5.7.1 =dev-qt/qtgui-4.8.7 =dev-qt/qtcore-5.9.2 =dev-qt/qtwebchannel-5.7.1 =dev-qt/qtpositioning-5.9.2 =dev-qt/qtopengl-4.8.7 =dev-qt/qtcore-4.8.7-r2 =dev-qt/qtwebengine-5.7.1-r2 =dev-qt/qtgui-5.7.1 =dev-qt/qtsql-5.9.2 =dev-qt/qtprintsupport-5.7.1 =dev-qt/qtdeclarative-5.7.1 = dev-qt/qtxmlpatterns-5.9.2 =dev-qt/qtdbus-5.9.2 =dev-qt/qtsvg-4.8.7 =dev-qt/qtopengl-5.7.1 =dev-qt/qtxml-5.9.2 =dev-qt/qttranslations-4.8.7 =dev-qt/qtdbus-4.8.7 =dev-qt/qtchooser-0_p20170803 =dev-qt/qtwebkit-5.7.1 =dev-qt/qttest-5.9.2 =dev-qt/qtnetwork-5.9.2 =dev-qt/qtsvg-5.7.1 =dev-qt/qtscript-4.8.7 =dev-qt/qtconcu rrent-5.9.2 =dev-qt/qtx11extras-5.7.1 >>> 'Selected' packages are slated for removal. >>> 'Protected' and 'omitted' packages will not be removed. Would you like to unmerge these packages? [Yes/No] Yes Next, run this command:
 
# Here I have renamed the /usr/portage directory for backup emerge -av @preserved-rebuild  

Holy cow, I have a local version of dev-libs/glib-2.50.3-r1. Moved that out of place and the update could start. Wonder why I created the most challenging upgrade for myself. Lesson learned: When there is a conflict, check , really check where it comes from. I was assuming that both gdbus-codegen and dev-libs/glib come from the same repo, but later found out that dev-libs/glib comes from another repo.

This does the trick:
euse -E pulseaudio # enable pulseaudio feature globally # to be sure I also installed alsa-oss. Don't have time to check if it is really necessary. emerge -auDN @world # update and recompile all packages that uses pulseaudio # reboot and run alsamixer to make sure pulseaudio is unmuted. Case closed.