Comment 4 for bug 793380

I found how to delete all notes from the server:
https://wiki.ubuntu.com/UbuntuOne/FAQ/HowCanIDeleteAllMyTomboyNotesFromTheServer

I also tried to re-authenticate Tomboy with the steps here:
https://wiki.ubuntu.com/UbuntuOne/Bugs

Sure enough, Ubuntu One notes are wiped out, and tomboy is now uploading all (backed up, local) notes to Ubuntu One server.

However the process failed with another exception:

** (Tomboy:29124): DEBUG: SyncDaemon already running, initializing SyncdaemonDaemon object
[DEBUG 21:56:35.147] SyncThread using SyncServiceAddin: Ubuntu One
[DEBUG 21:56:35.155] Building web request for URL: https://one.ubuntu.com/notes//api/1.0/
[DEBUG 21:56:43.365] Building web request for URL: https://one.ubuntu.com/notes/api/1.0/user/
[DEBUG 21:56:50.601] 8
[DEBUG 21:56:50.602] Sync: GetNoteUpdatesSince rev -1
[DEBUG 21:56:50.604] Building web request for URL: https://one.ubuntu.com/notes/api/1.0/op/?include_notes=true
[DEBUG 21:56:55.129] Sync: 0 updates since rev -1
[DEBUG 21:56:55.131] Building web request for URL: https://one.ubuntu.com/notes/api/1.0/op/
[DEBUG 21:56:59.774] Sync: Uploading 740 note updates
[DEBUG 21:56:59.927] Building web request for URL: https://one.ubuntu.com/notes/api/1.0/op/
[DEBUG 21:57:03.605] Building web request for URL: https://one.ubuntu.com/notes/api/1.0/op/
[ERROR 22:00:35.681] Caught exception. Message: The remote server returned an error: (504) Gateway Time-out.
[ERROR 22:00:35.684] Stack trace for previous exception: at System.Net.HttpWebRequest.CheckFinalStatus (System.Net.WebAsyncResult result) [0x00000] in <filename unknown>:0
  at System.Net.HttpWebRequest.SetResponseData (System.Net.WebConnectionData data) [0x00000] in <filename unknown>:0
[ERROR 22:00:35.686] Rest of stack trace for above exception: at System.Environment.get_StackTrace()
   at Tomboy.WebSync.Api.OAuth.MakeWebRequest(RequestMethod method, System.String url, System.Collections.Generic.List`1 parameters, System.String postData)
   at Tomboy.WebSync.Api.OAuth.WebRequest(RequestMethod method, System.String url, System.String postData)
   at Tomboy.WebSync.Api.OAuth.Put(System.String uri, IDictionary`2 queryParameters, System.String putValue)
   at Tomboy.WebSync.Api.UserInfo.UpdateNotes(IList`1 noteUpdates, Int32 expectedNewRevision)
   at Tomboy.WebSync.WebSyncServer.CommitSyncTransaction()
   at Tomboy.Sync.SyncManager.SynchronizationThread()
[ERROR 22:00:35.686] Synchronization failed with the following exception: The remote server returned an error: (504) Gateway Time-out.
  at System.Net.HttpWebRequest.CheckFinalStatus (System.Net.WebAsyncResult result) [0x00000] in <filename unknown>:0
  at System.Net.HttpWebRequest.SetResponseData (System.Net.WebConnectionData data) [0x00000] in <filename unknown>:0

(Tomboy:29124): GLib-CRITICAL **: g_source_remove: assertion `tag > 0' failed

I will retry again.