Today, I finally decided to get back into Destiny 2 by buying Lightfall and Final Shape. I completed the timeline new light questline, but it appears my witch queen and beyond light progress was reset. I remember completing both questlines and having stasis on one of my titan account, but now, it's not there. Is this a common issue? Do I have to replay both questlines from the start again?
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Not a common issue. You have the WQ emblem on your warlock equipped, is it possible you completed it on that character instead of your titan? Personally I get my character questlines mixed up all the time.