Got the newest patch update today. Went to start up a game, my old custom faction was gone so i decided to remake it (Not in the available faction selection box). However when i entered in the Faction name "Terran Empire" it said it was in use "Your faction name has already been given to an existing faction". 

I suspect although my old custom faction is no longer playable in the newest patch the game still thinks its active and won't allow me to use the same name. Any fix for this? A minor thing but annoying as i tend to name all my empires roughly the same, heh. Thanks

The only way I've found to fix this is to delete the faction file manually. You can find it here on Windows:

C:\Users\YourUserName\Documents\Endless Space 2\Custom Factions

In there, there should be a .xml file with the name of your old faction. If you delete it or remove it from this folder, you should no longer have this conflict when creating a new faction with the same name as your old faction.

Thank you! That solved it, I was looking under/documents/my games as most games usually default there heh (or hiding somewhere in appdate, ugh).