Yes, the secrecy of the ballot is protected in an online election with Polyas.
After logging on to the online voting system, an anonymous token is generated with your access data, which does not allow any conclusions about the identity of the voter. You will cast your vote using your token; your access data will not be further transferred. After casting your vote, your token will be deleted and the electoral roll will be notified, that no new token can be generated for this access data.
That is how the electoral roll knows that you took part in the election but not how you have voted. The digital ballot box knows that the ballot paper was filled out but not by whom. You are the only one who knows this secret.
The secrecy of the ballot is maintained according to the electoral principles.