I overwrote the directory to upgrade from 2.0.5 to 2.0.6...
I'm not sure that is a safe way to update. Have you tried to unzip the release in its own folder and run?
Tosch110 may have a say about this, so I'm cross posting in the SN Lite release thread.
I'll use the new lite client & superBTC next time then, it's weird that the order book for those is empty though.
If it's too much of a hassle to run the old mgwBTC you might return me the BTC if it's possible, then I'll use the superBTC 
Of course we're running the mgwBTC, and anyone who sent a deposit will receive the assets. And of course anyone who holds mgwBTC can swap them for superBTC. I just hope that the old MGW servers will cooperate a bit more and help to automate the coin migration process, because doing manual multisig transfers in Bitcoin can be a pain and very time intensive. And the faster we can move the coins to the new wallets, the better.
The superBTC orderbook is understandably empty because very few BTC have been deposited so far in the SuperNET MGW. The same thing happened last year when development servers phased out. But as old servers go offline, the activity will move over. It's also much easier to know that, for as long as BTC/NXT block times are not unusual, depositing or withdrawing can take half an hour.
Don't worry, you'll receive your deposit. Then you can either sell in the AE or withdraw it back to a deposit address in the new servers (see
how to swap mgwBTC to superBTC). If you do the latter, just keep in mind that processing time for withdraws through old servers is quite unpredictable, but once you're using superBTC, you'll have a much better service.