I hope the swap does not involve taking all eBTC out of Etherdelta and other exchanges. The fees are already killing in the normal way.
It really depends on the exchanges. I would advise to keep them out of exchanges even if a clean swap is promised. Some time ago FUCKtoken swapped to new contract. Nova Exchange played asshole, didn't update their contract and several people lost their FUCK tokens.
I'm sure everyone will have enough time to transfer all eBTC tokens to MEW (or any other compatible) wallet. Just stay tuned and read the announcements.