Microsoft warned that “a problem can cause some or all of the replicas of a public folder to unexpectedly disappear when changing the replica lists on Exchange 2010. This can happen when using Exchange 2010 RTM Public Folder Management Console, Set-PublicFolder CMDlet (or scripts that call it) or ExFolders tool connected to Exchange 2010 RTM server. If only some of the replicas disappear, you may try to add them back, only to see them instantly vanish again. If all of the replicas disappear, you must restore public folder data from a backup.
This’s due to a bug in Information Store in 2010 RTM. When Store receives the new replica list from the admin tools, under certain conditions it makes the wrong decision about which replicas are supposed to be added and which’re supposed to be removed. This bug has been fixed in Exchange 2010 SP1 (or here) Store.”
This behavior will only affect folders that were originally created when Exchange 5.5 was present in the environment, so you typically only see this on very old public folders.