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Hi from just answer. I'm PDtax, and will assist.
The IRS lock in program is based on their assessment that you did not have enough tax withheld. Since you were a nonfiler, using this mandate for withholding will get your attention.
Since you are now in compliance, and have filed, you can fix things. You will have to complete a new w-4 and send it to IRS for approval. The instructions and address to mail it should be in your letter. I would enclose an explanatory letter, and copies of pages 1 and 2 of your recently filed forms 1040. Write "DO NOT PROCESS" on the tips of the 1040 pages you enclose.
Send it certified mail, return receipt. IRS should approve quickly.
If two weeks passes with no changes, of if the excess withholding causes a hardship, you can ask for relief using a form 911, Taxpayer Assistance Order.
Thanks for asking at just answer. Positive feedback is appreciated. I'm PDtax.