I deleted the messages directory and its subdirectories.
I deleted "mq_persist_Joram_5.1.0_127.0.0.1".
I deleted the AS2_DB* files.
I restored the original "certificates.P12" file that came with the installation.
And this is the result:
[Jun 23, 2009 12:22:36 PM] Welcome, admin
[Jun 23, 2009 12:22:36 PM] mendelson opensource AS2 1.1 build 27
[Jun 23, 2009 12:22:42 PM] readKeystoreCertificates: PKCS12 key store mac invalid - wrong password or corrupted file.
I found the right configuration file buried under the /root/.java and was able to reset that so I could start up with the original configuration.