The skins/ custom overrides was actually the only sub-directory (beside IM and chat logs, of course) shared by the Cool VL Viewer with other viewers for its files. All the rest (settings, cache files, login hashes, etc) is kept in separate directories or in files with an entirely different name, to avoid collisions...
In next release, I changed the custom skin overrides directory name for "cvlv-skins", and the viewer will inform you (once only) via a notification if it finds a "skins" override directory but no "cvlv-skins" directory along it, so that you know you need to either rename or copy the old directory.
This way, you can keep sharing safely ~/.secondlife with other viewers (which is desirable to avoid loosing the continuity in IM and chat logs, if you use several viewers with the same account).