It sounds like your employer might be in hot water, but unfortunately you are the one being inconvenienced.
The IRS suggests you wait for them to investigate, and you may also contact Taxpayer Advocate Service (TAS) for help. TAS service is free and they are part of the IRS, so they should be able to get answers fairly quickly.
You can reach TAS at 877-777-4778
IRS link to letter 4464C
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