Hello there,
I would like to inform you that, as stated in the > MERGE FAQ < , when you have to merge your account, you have two options:
Choose the one where you played and had all your story progress, and so keep all your badges and the story progress
Choose the other server where you never played on, and so you get all your story progress resetted.
However, both the options guarantee you to keep all your Pokemon and Items without any problem.
In my knowledge, PRO STAFF has the power to undone the merge(unmerge), but for further info i suggest you to be patient and wait for the reply of a member of PRO STAFF.
I would like to add to NOT MAKE ANY TRADE ON SILVER, because PRO STAFF can't unmerge if you have made any trade on Silver.
For now, just be patient until a member of PRO STAFF will reply.
Hope this helped you a little, have a great day !