If you have CFP 3 installed, And want to keep your previous configurations, Here is what you do when upgrading from CFP 3 to CIS 3.5 to keep your original settings.
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Miscellaneous>Manage my Configurations>Export Your configuration file to anywhere on your Hard Drive, For example my Documents, Desktop, etc. You can also rename it.
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Uninstall CFP 3.0, Reboot, Download & Install CIS 3.5, Reboot. Now go back to Miscellaneous>Manage my Configurations>Import And import your configuration file where you saved it. When you successfully imported it, Make sure you Select that Configuration in Manage my Configurations. Delete any other Default Configurations you DON’T use, Like Proactive Security, Antivirus Security, etc which just modifies your policies & Settings.
When you have imported Comodo Firewall configuration, note that the profile contains old FW executables location. You need to correct it.
Go to Defence+>My Protected Files>Groups… Then replace in Groups
-Comodo files/folders and
-Comodo Firewall Pro paths
from C:\Program Files\Comodo\Firewall
to C:\Program Files\Comodo\COMODO Internet Security\
Also include file C:\Program Files\Comodo\COMODO Internet Security\cfpconfg.exe
Now your settings from CFP 3.0 should work! Note: You CANNOT do this for COMODO Antivirus v2.0 Beta & v3.5, It only works for COMODO Firewall & Full CIS.
31/10/08: COMODO Firewall 3.0.25.378 now Updates to COMODO Firewall automatically or manually (Though the update doesn’t include the Antivirus, Just the Firewall.) If you want full CIS, Please follow instructions above. 
If you have any questions or concerns, please contact myself or any online Moderator.
Thanks
Josh