When a business receives an Employee Retention Credit for a prior year, the prior year tax return(s) must be amended. The 1120S will be amended by increasing the salary and wage deduction on Line 8. Any interest included in the credit will be report on Line 5. Of course, the amended 1120S will produce amended K-1 forms for each shareholder at which time the shareholder will need to amend the 1040.
When the shareholder amends the 1040, if additional tax is due then that tax must be paid as soon as possible. However, the IRS has announced that there is relief from interest and penalties if there is reasonable cause.
https://www.irs.gov/newsroom/irs-reminds-employers-of-penalty-relief-related-to-claims-for-the-employee-retention-credit