This Knowledgebase article provides detail about the "File System has been marked as in sync" message.
The 'File System has been marked as in sync' message appears when the 'Full Mark State as In Sync' button from the 'Files Synch and Verify' tab of the 'Data' section has been pressed.
The 'Full Mark State as In Sync' feature marks all files as synchronized without performing the block level check of each constituent file in the file filters. This feature is helpful when the data structures are known to be identical between the servers. The file can then be manually synchronized later when network traffic and file replication is light.
Note: Marking files or folders as synchronized using the 'Mark State as in Sync' or 'Full Mark State as in Sync' buttons does not mean that the passive server data is a true replica of the active server data. Neverfail recommends that if files or folders, known to be out-of-sync, are marked as synchronized, a switchover not be performed until the data is verified and synchronized; otherwise, data corruption may occur.