You will want to read the whole Update thread - but the key part to take away is you have not actually lost anything.
Problems with Account Merge (Missing Player Items/Data)
Tl;dr: You have not lost any items or progress, though some players are logging in and seeing some/all elements missing from their collection.
In all cases, no player data has been wiped or lost. We have a client-side fix for this that cannot be deployed until next week, so we are exploring server-side fixes and will provide updates as more information becomes available.