Running into it here too now on LFR. Only on Wrathion, or at least I have to bail there. Done a log on-log off, client reset, “scan & repair,” reset Battle.net & even a total shutdown & startup (cold boot). I ran each of these scenarios w/o luck. This was not a problem on previous runs this week, only today.
Update: Wrathion & raid all showed up on 9/9/20 after servers came up. On 9/10/20 back to shadows on floor of only the raid members. The same bug occurred when I went in on the same toon I did LFR on the previous day. Like before, everything is up to date on PC and it is not toon-spacific. problem started 24 hours after weekly servicing.