I have not use e-coin in almost a year, because when I try to transfer my paypal funds to bitcoins they but a hold on my virtual card. I had about $45 in bitcoin in the account. I decided to check the account after 8 months because price of bitcoins have went up several folds, only to find out there is no bitcoins in the account.Avoid them like the plague.
If you had stored bitcoins with them then nothing should have been deducted from that amount. It is only possible for your balance to be reduced if you are issued a VCC and you stored your BTC there, but since you said that you only went on the site again because bitcoin price has gone up, i think you have definitely stored your money in the wires bitcoin wallet.
E-coin to wirex rebranding shouldn't have affected you, either.
Contact their support and see what has happened. Very strange indeed.