This is due to a change we had to make in 6.01; to fix it, please reinstall Sapphire v6.0 and open your affected project.  Go to every Sapphire Plug-ins that contained a different custom flare and save a preset.  Now when you go to Sapphire v6.01, you will be able to re-load your custom Flare from inside the Preset Browser.  

Warning, if you have lost your custom Flare in v6.01, do not save over your old project file until you've recovered your custom Flare or you may lose the custom Flare!  This incompatibility was unavoidable and we're sorry for any trouble it causes.