It seems that Pokemon GO players are dealing with yet another bug/glitch in the game. This specific bug/glitch apparently makes the Shiny Pokemon disappear from your Pokemon list and PokeDex.
One player reported that she had a Regular and Shiny form Pokemon (in her case she lost Gyarados), which have now disappeared like she never even had them. There are other reports that this happened with other Pokemon too, Mudkip, Skarmory, and many more.
— Lacey Meredith (@laceyellen97) February 14, 2021
Here are some more reports from players who commented on the thread:
I swearrrrr I had a shiny skarmony but it’s gone now. Also in my pokedex it says I had a shiny (regular and galarian) meowth and never caught that
The same happened with my daughter’s too. She had a shiny Vermouth and it is now gone.. kicker is she hasn’t played in a few months and when she went through them it was gone. Niantic wouldn’t replace it.
Wow. I thought I was going crazy. A couple months ago my shiny machop disappeared. I just thought maybe I transferred by accident but I swore I hadn’t because it was a favorite.
Same thing happened to a buddy of mine. He put a 4* rhyperior in a gym and a few days later he got the notification it had been kicked out and he got the coins but it never came back to him. It just disappeared
We currently have over 500 Shiny Pokemon available in the game, which is a big number, but not enough, since it is so hard to find them as either wild spawns or hatches from eggs.
This bug that makes them disappear is making the situation worse than it is already.
We’ve never seen anything like this before, and we do believe that Niantic and Pokemon Go can’t really help or solve the situation as they don’t have any data about players’ Pokedex. We advise you to open the game and check on your beloved Shinies.