The official response from blackberry support:
Hello,
Thank you for contacting BlackBerry Application Development Support.
This error means the keys have already been registered so cannot be registered again. To have this issue resolved a new set of signature keys will need to be issued and installed. Please note that signature keys are now completely free and issued several times a day, so the fastest way to get a new set would be to place a new order:
https://www.BlackBerry.com/SignedKeys
Prior to installing this new set of keys please first delete all present CSI files as well as the sigtool.* (DB, CSK, SET) files that will reside in the sub-directories of all development tools. Make sure to write down the PIN used to place the order as well, it will be needed when installing the keys.
After registering your keys and verifying that they are able to sign I would recommend backing them up some place safe in case anything should happen to your development environment:
Go to the first URL and request a new set of keys. You should get an order confirmation email right away. In about 1-2 hours you will get 3 more emails. Each one will have a CSI key attached. (The keys are free to generate)
To avoid this issue in the future, you can back up the keys, according to the instructions in the second link (above).
Good luck!