Did you have to resubmit fingerprints or reference your paper application in any way? I am in a similar situation.
You do NOT not have to resubmit fingerprints. You DO have to ask that they retrieve what you have already sent.
The way the new eDO system works is a bit convoluted, but it does make sense. Just follow the instructions included on the website. You have to start over and resubmit your application and payment online. You then forward the confirmation email from that resubmission/ payment to the email address provided on the FBI website.
Be sure to add and include the info they request from the original mailed application when you forward the confirmation email (your address, phone number, the service used to mail your original application and tracking number) This allows them to dig into the stack of mail and locate your original application. They will retrieve the fingerprint card you already sent from that submission.
If you included a cashier's check for payment (like I did) they will send that back to you. I received my original check about one week after I received the email with the link to the police certificate pdf.
If you originally paid with a credit card, they supposedly will issue a refund to the original payment card.
I simply created a forward of the confirmation email and included the following text above the forwarded message body:
Greetings-
I previously submitted a request for a FBI Background Check by mail on December 22, 2017. It was received on Dec. 27, 2017. Please accept this request to process electronically.
The original mailed request contained the following information:
Mailing address: your address and zip code here
Telephone number: use the number you included on your original application
Carrier service: US Postal Service Priority Mail (or whatever carrier you used)
Tracking number: be sure to send the tracking number so they can locate your original submission in their stack of mail
Please locate this request and use the fingerprint card enclosed with the application. I understand the original certified check enclosed with the application will be returned to me at the address above.
Thank you,