Yes, I've had a similar experience with missing Void shards, it seems to be a bug or glitch of some sort that converts shards to champions seemingly automatically.
My problem was all my shards somehow ended up in the champions area as champions. One minute they were there and the next time I logged in they were gone.
Still not sure how this may have happened but it's very disappointing. The reply message I got from Support was ~
" There is no indication that your account was hacked or influenced in any way. We can not return items if they were already spent.
If someone else has access to your account in your household - change your password and credentials."
The Support team can't do much about this problem at the moment until more information comes to light as to whether this is a hacking job from an angry 12-year-old teenager or a technical bug of some sort. My guess is on a bug/glitch issue.
But at the very least I did get a very expedient reply which is better than no reply at all.