I know how painful it can be to get something corrected in the IRS's system. We had a similar experience on corporate taxes for SynaptiCAD, the first company we started. We opened up a second version of the company to switch from S corporation (passthrough tax entity) to a C corp (files taxes separately from its owners). That all went fine, but there was a brief period when both the old company and the new company were operational. On a tax filing for one company, we accidentally used the tax ID of the other company (I think this was for employment taxes we collected for the IRS, but it's been a while ago, so not sure). This was the only mistake on the form (we had the correct company name, etc), but I think it took many phone calls and almost a year to get it fully straightened out. Everything would seem good, then we'd get something else from them which made it clear it wasn't fixed everywhere. It's amazing how long it can take them to fix these kinds of minor errors.