Only if you register your public key. Otherwise, no, you'll lose your EOS tokens. It's all in their initial documentation they provided that users must register an EOS key. A lot of the fears people are circulating apart from this issue of registering your key is silly stuff they have come up with from lack of understanding of what is transpiring.
My view is if a person cannot grasp the EOS agreement, why it was written that way, and reasonably understand what the outcome would be... why are they holding EOS tokens or buying them?
It would kind be like owning bitcoin without understanding what a blockchain is or what cryptocurrencies are. A lot of people just throw money at stuff these days without understanding what it is they are buying. I own some EOS, I registered my key, and I understand what is going to happen, and I fully grasp why their agreement was written as such, and I can foreseebly understand the outcome that will create. Whoever controls the eos github address, and publishes the list of EOS token holders, ultimately decides the EOS token holders. Such a publication would be verifiable against the Ethereum blockchain itself. Certainly, anyone could launch any modified version of EOS they wish, but only those running the official github version with that list of token holders would be considered the legitimate EOS by all parties: developers, exchanges, ect.
Other variant versions of EOS would not meet consensus with the official network and would be forks.