Accurate delay-Doppler channel estimation is critical for next-evolution waveforms (NEWs) to enable reliable signal detection. This paper proposes a robust channel estimation algorithm that integrates Flag sequences optimized via an adaptive accelerated parallel majorization-minimization (AP-MM) algorithm with a proposed channel estimation algorithm. To enable efficient, low-complexity parameter extraction and further overcome the robustness issues of conventional greedy estimation, we introduce two key enhancements, i.e., a candidate selection strategy to mitigate spurious sidelobe peaks, and a global least squares (LS) refinement stage to eliminate error propagation caused by sidelobe masking effects. Numerical results demonstrate that the proposed scheme significantly outperforms traditional existing algorithms, achieving the desired estimation accuracy.