Basically it's happening because of the hard link to savegame folder that you (I assume) created to make BGEE work with outdated version of Shadowkeeper.
If you had a link to the saved games for some Shadowkeeper hack, then yeah, you lose them. But normally the updater wouldn't delete files outside the install directory.
The hard links are no longer necessary, use latest version of EEKeeper.
Comments
http://forum.baldursgate.com/discussion/22821/omfg-patch-wiped-out-my-save-directory-careful-guys-if-you-use-hard-links/p1
Basically it's happening because of the hard link to savegame folder that you (I assume) created to make BGEE work with outdated version of Shadowkeeper.
This is what devs said: The hard links are no longer necessary, use latest version of EEKeeper.
Thanks for the clarification