I read it if you withdraw the 55%, you accept the 45% as tokens (not you lose it).
Depends on when you withdraw.
Tomorrow, on September 2, 2017, it will be possible to withdraw 55% of the funds from the account in koins on the condition that our debt obligations are abandoned to the remaining 45% of funds in the form of tokens.
So if you cash out 55% tomorrow, BTC-e are not obliged to give you tokens for the remaining 45%, so you take a 45% hit.
Look at it as the "withdrawal fee from hell" for those that are impatient.
BTC-e is probably smart to do it this way. It is expected that there will be an exodus. The users that would immediately leave upon relaunch would crash all the markets trying to get BTC out otherwise. Now they can separate exiting users (including most US users), and give them less back. And they will give their "loyal" customers more back, showing goodwill and encouraging them to stay on the new platform. This should bring some stability to their markets upon relaunch.