A defeated faction can be restored once a lord of this faction gets a town or castle after he switches to other factions. All lords of this faction including the king will come back, and the defeated faction is restored.
This mechanic is not included in the list of Floris mods and cannot be disabled through the Floris options.
Removing Kingdom Restoration Edit
To remove kingdom restoration from Floris, there are two ways:
the source dev kit will need to be downloaded for Floris. The file module_simple_triggers.py in the source folder of the version that you are using will need to be edited to remove the restoration trigger.
The easiest method to avoid save game issues is to simply remove the text between the open and close brackets [ ]. It's important to leave the brackets so the game still thinks there is a trigger included, as the game checks the save game against the number of triggers in module_simple_triggers.py. The text to remove can be found here: http://forums.taleworlds.com/index.php/topic,68861.0.html
Only the trigger in module_simple_triggers.py needs to be changed. The module_game_menus.py code should not be invoked if the trigger is removed.
Once module_simple_triggers.py is edited, save the file. Compile the version you are using and that you should have edited (expanded or gameplay for example) using the respective .bat file. First, make a backup of the Floris files located in your Warband module folder. Then, copy all of the generated files into the Warband module folder where Floris is located.
Assuming no issues, the restoration effect should now be removed.
As instructed on this Reddit-Page
search the file
\Modules\Floris Mod Pack name\simple_triggers.txt
make a backup, open in text editor, search for the line starting with
24.000000 45 6 3
(there are two spaces after the '24.000000')
(This line-block should be preceded by a line that starts with '24.000000 53 1602'... and followed by one with '1.000000 18'...)
and then delete all numbers in this line after the '24.000000' and replace them with '0' so the whole line-block reads
(keep the two spaces after the '24.000000')