I had somewhere around 100 rune of shattering, then all of a sudden I realized I was at 0, after acquiring 10 more and transferring them to the crafting items, they all disappeared again. I’m at 0 again.
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Also losing glyph of hope as well when transferring. 
happened to me too
We’re working on a fix and we believe it’s just a visual issue.
Visual issue, but you can’t use the shards when it’s at 0.