So I just had a very weird occurrence on our portal.  We have the SynchronizeFiles event fire off every now and again because we have a load of files we link to in all sorts of modules (Links module for the link icon, for example, and all sorts of other modules in general).

The files just got all renumbered for us today out of the kindness of the synchronizer... yet the folder ids stayed the same.  How about that?

I can't roll back the database because we have too much new data added each day; so I've written some queries and updated everything the best I can (some manual things gonna still have to be done).

Question is, how in the world did this happen and what can I do or could I have done to prevent it? 

Sad thing, that folder has somewhere around 600 files in there.

The Schedule History for that event shows a failure as such:

DotNetNuke.Services.FileSystem.SynchronizeFileSystem, DOTNETNUKE 
File System Synchronization failed. System.Threading.ThreadAbortException: Thread was being aborted. at DotNetNuke.Services.FileSystem.FolderController.GetMappedDirectory(String VirtualDirectory) at DotNetNuke.Entities.Portals.PortalInfo.get_HomeDirectoryMapPath() at DotNetNuke.Services.FileSystem.FileInfo.get_PhysicalPath() at DotNetNuke.Common.Utilities.FileSystemUtils.RemoveOrphanedFile(FileInfo objFile, Int32 PortalId) at DotNetNuke.Common.Utilities.FileSystemUtils.RemoveOrphanedFiles(FolderInfo folder, Int32 PortalId) at DotNetNuke.Common.Utilities.FileSystemUtils.SynchronizeFolder(Int32 PortalId, String physicalPath, String relativePath, Boolean isRecursive, Boolean syncFiles, Boolean forceFolderSync) at DotNetNuke.Common.Utilities.FileSystemUtils.SynchronizeFolder(Int32 PortalId, String physicalPath, String relativePath, Boolean isRecursive, Boolean syncFiles, Boolean forceFolderSync) at DotNetNuke.Common.Utilities.FileSystemUtils.SynchronizeFolder(Int32 PortalId, String physicalPath, String relativePath, Boolean isRecursive, Boolean syncFiles, Boolean forceFolderSync) at DotNetNuke.Services.FileSystem.SynchronizeFileSystem.Synchronize() at DotNetNuke.Services.FileSystem.SynchronizeFileSystem.DoWork()

Not good to hear.  I know they (HR department) added a new folder under the folder in particular that had the problem but a subsequent refresh worked fine.  We've been running DNN since 4.4.1 and this is the first time it has happened.

Hopefully somebody can shed some light.

Beautiful.  So it is a known issue of some sort; the thread died off several months ago but the problem seems to persist randomly.  One thing Sebastien said that made me think was something to the effect of "perhaps the scheduler is running at the same time as another instance" and that could actually be my problem.  I have both auto-sync and the scheduler turned on.  Additionally, right about the time of failure I installed a new version of a module so it could have caused the scheduled process to die and then start up again.  Ouch!

I'm going to turn off the scheduled process and let the admins know they should manually sync up when necessary.