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Blizzaru - I think the SWF resets your faction choice. So you need to the re-choose faction for your progress to be fixed. You can re-choose a faction by doing the following:
Go to swordhaven ---> Queen Victoria --->The Greenguard Alliance ---> Choose your faction : The Rose, The Golden Hand or The Vind.
Please can you tell me if this fixed everything? Can you go to the last Bk3 quest, 'In Search for Slayers'?
Also can you tell me what your win streak is for A.A.R.G.H?
What floor level are you on for the Tog Endless Invasion?
Do you have the Dragon PVP badges? Do you want these?
Are the custom armours from the 'Inn at the Edge of Time' all unlocked?
Are your saved custom armour choices reset?
Also, did you interrupt the SWF at any point? I believe, the SWF needs a couple seconds (upto 20 seconds) to complete.
Have you observed anything else that seems anomalous?