It depends. The IRS is in the process of renewing certain ITIN numbers. Once the number has been renewed, efiling is allowed according to the IRS. The program, however, cannot account for whether or not your ITIN actually has been renewed or not, so it will provide this warning.
Therefore, if the program will not allow you to efile because of this diagnostic, go ahead and mail-in the return. Since you have the acceptance letter from the IRS, you will not need to prepare another W-7. You can be confident that the IRS will accept the return.
On the other hand, if it is only a warning message, then you may attempt to efile, and it should not be rejected for being an expired ITIN. (Cannot guarantee that there might not be another reason for the return to be rejected, however). Here is an IRS website that explains a bit more on this: https://www.irs.gov/individuals/itin-expiration-faqs
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