The 4.0 EAP tends to do a full uninstall before installing (it’s pre-beta, pre-alpha even; so it’s no wonder).
This tends to blow away your settings changes. If that’s a pain point for you, the settings are stored in “%userprofile%\application data\jetbrains\resharper\v4.0\vs9.0”. There are a couple of xml files in there that store your settings. Before you upgrade to the latest build, just copy those to another directory.
It’s very likely that the format of these files has changed since the last build so copying the backups over the new version could possibly make Resharper to blow-up. So, use with caution.