If you did encounter this exclusion list issue all you have to do is upgrade to the newest 188.8.131.5219 build of Immunet and your Exclusion list will be restored. This build also has some other improvements, bug fixes & with the infrastructure change occurring I would definitely recommend to anyone that's running a earlier version to upgrade ASAP.
I got this new build seamlessly installed right through the UI (a re-start is necessary after installation) or you can download the latest 184.108.40.20619 bootstrapper installer package here if you wish to install it manually yourself. https://download.immunet.com/binaries/immunet/bin/ImmunetSetup.exe
More info about this new build can be found here at this Announcements topic. http://support.immunet.com/topic/3723-new-release-v624/?_fromLogin=1