You can perform a search to find all flagged messages:
List<long> flagged = imap.Search(Flag.Flagged);
You can examine Flags collection after using Imap.GetMessageInfoByUID method:
List<MessageInfo> infos = client.GetMessageInfoByUID(client.GetAll());
MessageInfo first = infos[0];
bool isFlagged = first.Flags.Contains(Flag.Flagged);
You can also use Imap.GetFlagsUID method to get flags for particular email.