I had that same issue last year in the S-Corp module. It was very nerve-wracking. I bird-dogged the FTB MyFTB page for my clients at the PTET payment deadline to make sure it went through.  The payments went through for all of them.

I know that doesn't give much assurance or comfort, but that's all I have for you. If the Client Letter says they will be auto-debited, I think you're all set.