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You will use Form 941-X to correct errors on a Form 941 that you previously filed.
If you have not previously filed then you would just use 941 and not 941-X.
It will be best to contact the IRS office that sent the letter to confirm this was an estimated return that does not need to be amended 941-X but actually needs to be filed on 941.
In almost all cases any amend or difference to the proposed change is best sent to the office that has proposed their change (or estimate) so they will immediately apply your change (rather than an amended return going to the usual other location to be amended and being apparent to the letter sender.)
Form 941-X is available at http://www.irs.gov/pub/irs-pdf/f941x.pdf
Instructions for 941-X are online at http://www.irs.gov/instructions/i941x/ch01.html
"If you did not file a Form 941 for one or more quarters, do not use Form 941-X. Instead, file Form 941 for each of those quarters"
Instructions for 944-X are online at http://www.irs.gov/instructions/i944x/ch01.html
You do want to confirm that the change from 944 to 941 is needed on paper in your case. Again, the IRS office that sent the letter may be the best place for that confirmation.
In my experience this change has been able to be made, in some cases, by the IRS office without filing additional forms if the correct tax had been paid in full.
When changes are made for federal employment taxes it is often necessary to make changes to the state employment forms filed, as well.
You should coordinate and confirm with the IRS (at the contact information on the letter) where and what to change before sending anything or engage a tax practitioner with experience in these matters (such as an Enrolled Agent) if you prefer not to handle it yourself.
Please ask if you need more discussion or clarification.