SureAI

Skyrim updated this morning for me and I launch enderal and it was all fine until I tried to load my last save, for some reason it has put me in the inn where Delphine is in the base skyrim, is this due to the update or is it something entirely different?

Moved to support.
There was no Skyrim update. Did you hit the "Verify Integrity of game cache" button?
Does it synchronize your savegames?
Could you check out your savegame folder which saves are in there - only Skyrim saves or Enderal saves or both?
Savegame are located here: documents\mygames\skyrim\saves
We recommend to turn off the synchronize function in steam for Skyrim as long as Enderal is installed.

no I logged into steam and there was a 4.6gb update for some reason :/

Well, that's strange .. why would it update? Did it automatically download some mods which you have subscribed to?
The only way to get Enderal going again is a complete reinstall.
Backup your saves.
Uninstall Enderal completely (not archiving) through the Launcher and clear the skyrim folder by hand. Then download Skyrim again from Steam. Verify the integrity of game cache on Skyrim. Start Skyrim once and check if everything works. Then quit Skyrim and install Enderal from the installation package again.
Be careful about loading your savegames. They could be corrupted through loading in the Skyrim worldspace.

re-installing everything now so hopefully it works, thank you for the help