What to do if the IRS doesn't know how much I owe?

You can reach out to the IRS Taxpayer Advocate, after the current government shutdown is over. You can also try the online account services.

That said, the staffing issues with the IRS and the level of support it provides to taxpayers are unlikely to get any better since the DOGE wrecking ball was applied to it:

The Treasury Inspector General for Tax Administration reported this month [April 2025] that by March, the IRS’ workforce shrank 11%. This reflects the number employees who accepted the administration’s voluntary resignation offer to step down from their posts in exchange for receiving normal pay and benefits through the remainder of the fiscal year ending September 30. It also incorporates probationary employees who received termination notices in February following the Office of Management and Budget’s guidance on reductions in force (RIF).

Several lawsuits have been filed challenging the legality of the government workforce mass firings. One such complaint, filed April 28 by the American Federation of Government Employees and other labor unions in the U.S. District Court for the Northern District of California, cited an IRS memo dated April 15 detailing a Treasury RIF that would reduce the IRS by 40%.

Some former IRS employees said:

The IRS has been targeted early and often in the nascent days of the second Trump administration, with more than 7,000 probationary employees dismissed from the agency and promises of much more to come.