When I was inside counsel to a big recordkeeper, I saw this problem often, especially with healthcare employers.
If the § 403(b) and § 401(k) plans’ investment alternatives are identical (or nearly so) and one recordkeeper serves both plans, there might be a straightforward correction.
Even if the facts allow an ERISA § 403(c)(2) mistake-of-fact return to the employer, it can be unhappy because it’s work—often four layers of computations and reprocessing—and the employer can be exposed to restoring investment breakages that resulted from the employer’s mistake.
Instead, the recordkeeper corrects both plans’ records (including for each affected individual account) so every account and subaccount shows the correct number of investment fund shares. There is no payment of money, only corrections of records of beneficial ownership of investment fund shares. (I assume neither plan had shareholder-of-record ownership.) Done methodically and thoroughly, all records will remain in perfect balance.
Employers instructed these records changes without seeking any IRS approval.
Of those that later attracted attention (in the 1990s there was a wave of IRS audits of big healthcare systems), the IRS accepted what was done. For most, the IRS examiner without hesitation accepted what was done. For a few, I persuaded the examiner or supervisor that an employee could not have an elective deferral under a plan to the extent she was ineligible to so participate, and that the employer could not have made a contribution allocable to what could not have been an elective deferral.
Under equity law, a person or entity does not keep property if it in good conscience belongs to another.