Just did a full raid start to finish on my warlock. Went back to the tower to get my powerful engram and when I got there all of my milestones were gone. My hunter and titan still have their milestones intact, but my warlock's milestones are completely gone. Even on the destiny companion app under character progress its just a blank page. This happened immediately after the raid and seeing as my other two characters weren't affected I'd say it has something to do with completing the raid
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Milestones are sometimes not updating for me either. The quick fix is to go into orbit then it should update then go back to where you need to go. I made a new character got it to 20 and it wouldn't let me do nightfall after I have completed the strikes. This is an issue that has seems to have arisen from the patch.