I have the same error and cannot remove BAM since I'm using it.
When I try to re-initialize I get these errors:
2008-04-25 20:57:45,078 INFO [STDOUT] [INFO ]Import is skipping Recovery Logger [DEFAULTRECOVERYLOGGER] because it already exists in metadata.
2008-04-25 20:57:45,078 INFO [STDOUT] [INFO ]Import is skipping Dashboard Profile [system."Dashboard Profile"] because it already exists in metadata.
2008-04-25 20:57:45,078 INFO [STDOUT] [INFO ]Import is skipping Folder [VC_System.branding] because it already exists in metadata.
2008-04-25 20:57:45,078 INFO [STDOUT] [INFO ]Import is skipping JDBC Agent [adobe] because it already exists in metadata.
I'd delete if I knew the schema.
I turned off Enable Checkpoint in bam.properties but that didn't help.
Any ideas?