Расширить систему SftpSubs и заставить использовать протокол 3.0.
public class MySftpSubsystem extends SftpSubsystem {
@Override
protected Reply doProcess(Request request) throws IOException {
if (request instanceof SshFxpInitRequest) {
SshFxpInitRequest sshFxpInitRequest = (SshFxpInitRequest) request;
request = (Request)(new SshFxpInitRequest(3));
}
}