When you import your keys into the Graphene wallet you will see some extra accounts in your wallet.

usd-collateral-holder-#

These accounts will have an open margin position where you can adjust the collateral / cover.   

According to this article : https://bitshares.org/blog/2015/06/08/migrating-to-bitshares-2.0/, "All open orders will be canceled prior to the snapshot and their funds returned to their owners.". It's a bit old already, but I guess it's still valid.

Regarding BitAssets and short positions :
"Because the new chain is a simple migration and should retain all the same "perceived value", we can migrate all BitAssets and short positions. The snapshot date will be announced with 30 days notice so that any shorts that do not like the new BitAsset system can voluntarily exit. To ease your migration we recommend that everyone upgrade to BitShares 0.9.1 prior to the snapshot date and transfer 100% of every asset balance to yourself. This will consolidate your balances under a single account."

("transferring every asset to yourself" here means not keeping them on external exchanges)

Will everything be moved over to the new chain or is there any risk that an open short will cause problems?