System update removes desired file

I’m experienced with Linux but am new to Calculate & Portage. I wanted a copy of the Xephyr X-server which does not come with CLD, so I did my own emerge:

USE=xephyr emerge xorg-server

which worked and gave me a /usr/bin/Xephyr binary. Now, each time I boot CLD, I am notified of a system update (via graphical tool not cmd line) that has only a single package in it, xorg-server. If I accept this update, it runs successfully to completion but my previously-generated /usr/bin/Xephyr file has been removed. This cycle is repeatable. So last time before the update, I first made a private copy of Xephyr in $HOME, which survived the update process and runs fine. But this method can’t be the ‘real’ way to accomplish this. What is recommended? Thanks.

Hi Richard,
Save flag in your settings:

echo x11-base/xorg-server xephyr >> /etc/portage/package.use/custom