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It was happened to me when i turned trade locked things into gems. I couldn't find a way that time hope you can find.

If you have a card farming alt account, you can send your gems to it, and they will be combined. If you don't have one, send them to a trusted friend maybe? Moving them to another account works, simply trade them back to yours after that.

like eeev said currently only way to merge stacks of gems
and to avoid same problem in the future, never turn item into gems when still on "untradable / not tradeable" state