I’ve seen this happen when something in the employer’s QuickBooks records gets out of sync, but QuickBooks isn’t proof of whether the IRS actually got the money. It just shows what the employer entered or what their payroll service tried to send.
The only way to confirm the $68k is to check directly with the IRS and California. Your husband can request his Wage and Income Transcript, and it will show any tax payments tied to his SSN. California EDD can do the same.
On the employer’s side, they should have the EFTPS payment confirmation or the payroll filing (941, etc.). QuickBooks support won’t give them a letter, the proof has to come from their filings or bank confirmations.
I’d start with the IRS transcript. It’s the fastest way to see if the money was ever credited to him.
Robin Kon