Does the FY on the CP259 match that on the return as filed?  Are you sure of that?

According to IRS, you can e-file again:

What you need to do

• File your required business return immediately.
• If eligible, file your return electronically with all required schedules, using your e-file provider, or
• File a paper return with all required schedules.
• If you think you’re not required to file, complete the Response form enclosed with your notice and mail it to us, using the enclosed envelope or fax it to 855-800-5944. Use the Response form on your notice to explain why you don’t think you need to file.
• If you have filed within the last four weeks using the same name and EIN shown on the notice, you may disregard this notice.

https://www.irs.gov/individuals/understanding-your-cp259-notice