There's been some confusion about how to gracefully remove a public store on an Exchange 2007 server, so I want to briefly review the topic and hopefully clear up a particular point. In order to remove the store, you must follow the steps described in this previous blog post:
1. Move the public folder replicas to another server. There are several ways to do this which are described in the other post.
2. Associate mailbox databases with another public folder database. Again, these steps are described in detail in the other post.
3. Remove the PF database and delete the database files manually. This is the part that trips people up. Attempting to remove the database, they encounter this error:
Remove-PublicFolderDatabase : The public folder database specified contains folder replicas. Before deleting the public folder database, remove the folders or move the replicas to another public folder database.
Recall how this worked in Exchange 2003. When you removed a replica from a server, that server name was immediately gone when you looked at the replication tab in Exchange System Manager. However, the folder would persist in the Public Folder Instances view on that public store until all the data had replicated off. Removing the server from the replica list was only the start of the replica removal process, and ESM would not let you delete the public store until everything was gone from Public Folder Instances and the replicas had truly disappeared. The replica removal process and how to troubleshoot it was described in detail in part 3 of my replication troubleshooting series. That post describes Exchange 2003, but the process is the same in 2007.
Exchange Server 2007, Public Folder, Tips and Tricks