I activated all akonadi* and kmail occurence in kdebugdialog, then restarted akonadi in a console.

Browsing like always in folders containing unread mails, I sometimes see :
"QStringList Akonadi::NepomukSearch::search(const QString&) Calling blockingQuery() failed! 
QStringList Akonadi::NepomukSearch::search(const QString&) Calling blockingQuery() failed!", but it doesn't necessarily duplicates unread mails.
That doesn't help I guess, but I can't really see any special debug lines tied specifically to the problem when it appears in kmail..

I do get the usual " AkonadiAgentServer(14273) MaildirResource::itemRemoved: Item removed 379717  in collection : 625" repeated over and over when I use the function to delete duplicated mails.

~/.xsession-errors on the other hand is much more verbose. When entering a folder and seeing the duplicate bug happening, I get this :
kmail2(15566) MessageList::StorageModel::StorageModel: Using model: Akonadi::EntityTreeModel
kmail2(15566) Nepomuk::ResourceWatcher::start: Failed to connect to watch service "The name org.kde.nepomuk.DataManagement was not provided by any .service files"
kmail2(15566) KMKernel::instanceStatusChanged: A Resource started to synchronize, starting a mail check.
kmail2(15566) MessageList::Core::View::slotSelectionChanged: View message selected [ " Debian Project News - September 17th, 2012" ]
kmail2(15566) KMKernel::slotProgressItemCompletedOrCanceled: Last resource finished syncing, mail check done
kmail2(15566) KMReaderWin::setMessage: void KMReaderWin::setMessage(const Akonadi::Item&, MessageViewer::Viewer::UpdateMode) QSplitter(0x1c79610, name = "splitter2")
kmail2(15566) makeShowAuditLogLink: not showing link (not implemented)
kmail2(15566) KEmoticonsTheme::tokenize: Broken HTML entity, trying to recover.
...repeating 50 times...
kmail2(15566) KEmoticonsTheme::tokenize: Broken HTML entity, trying to recover.
kmail2(15566) MailCommon::SendMdnHandler::Private::handleMessages: AKONADI PORT: Disabled code in   void MailCommon::SendMdnHandler::Private::handleMessages()
kmail2(15566) makeShowAuditLogLink: not showing link (not implemented)
kmail2(15566) KEmoticonsTheme::tokenize: Broken HTML entity, trying to recover.
kmail2(15566) KEmoticonsTheme::tokenize: Broken HTML entity, trying to recover.
...repeating 50 times...
kmail2(15566) KEmoticonsTheme::tokenize: Broken HTML entity, trying to recover.
kmail2(15566) KMKernel::instanceStatusChanged: A Resource started to synchronize, starting a mail check.
kmail2(15566) KMKernel::slotProgressItemCompletedOrCanceled: Last resource finished syncing, mail check done
kmail2(15566) KMKernel::instanceStatusChanged: A Resource started to synchronize, starting a mail check.
kmail2(15566) KMKernel::slotProgressItemCompletedOrCanceled: Last resource finished syncing, mail check done"

sometimes I see that :
"kmail2(15566) MessageList::StorageModel::StorageModel: Using model: Akonadi::EntityTreeModel
kmail2(15566) Nepomuk::ResourceWatcher::start: Failed to connect to watch service "The name org.kde.nepomuk.DataManagement was not provided by any .service files"
kmail2(15566) KMKernel::instanceStatusChanged: A Resource started to synchronize, starting a mail check.
kmail2(15566) KMKernel::slotProgressItemCompletedOrCanceled: Last resource finished syncing, mail check done
kmail2(15566) KMKernel::instanceStatusChanged: A Resource started to synchronize, starting a mail check.
kmail2(15566) KMKernel::slotProgressItemCompletedOrCanceled: Last resource finished syncing, mail check done
kmail2(15566) MessageList::Core::View::slotSelectionChanged: View message selected [ "Upgrade to the New SourceForge; PeaZip Is POTM; Developers Wanted" ]
kmail2(15566) KMReaderWin::setMessage: void KMReaderWin::setMessage(const Akonadi::Item&, MessageViewer::Viewer::UpdateMode) QSplitter(0x1c79610, name = "splitter2")
kmail2(15566) MailCommon::SendMdnHandler::Private::handleMessages: AKONADI PORT: Disabled code in   void MailCommon::SendMdnHandler::Private::handleMessages()
kmail2(15566) KMKernel::instanceStatusChanged: A Resource started to synchronize, starting a mail check.
kmail2(15566) KMKernel::slotProgressItemCompletedOrCanceled: Last resource finished syncing, mail check done"

and sometimes that :
"kmail2(15566) KMReaderWin::setMessage: void KMReaderWin::setMessage(const Akonadi::Item&, MessageViewer::Viewer::UpdateMode) QSplitter(0x1c79610, name = "splitter2")
kmail2(15566) MailCommon::SendMdnHandler::Private::handleMessages: AKONADI PORT: Disabled code in   void MailCommon::SendMdnHandler::Private::handleMessages()
kmail2(15566) KMKernel::instanceStatusChanged: A Resource started to synchronize, starting a mail check.
kmail2(15566) KMKernel::slotProgressItemCompletedOrCanceled: Last resource finished syncing, mail check done
kmail2(15566) MessageList::StorageModel::StorageModel: Using model: Akonadi::EntityTreeModel
kmail2(15566) Nepomuk::ResourceWatcher::start: Failed to connect to watch service "The name org.kde.nepomuk.DataManagement was not provided by any .service files"
kmail2(15566) KMKernel::instanceStatusChanged: A Resource started to synchronize, starting a mail check.
kmail2(15566) MessageList::Core::View::slotSelectionChanged: View message selected [ "[Bug 283682] KMail duplicates filtered messages" ]
"/usr/bin/kmail(15566)" Soprano: "Could not connect to server at /tmp/ksocket-myuser/nepomuk-socket (Aucun fichier ou dossier de ce type)"
"/usr/bin/kmail(15566)" Soprano: "Could not connect to server at /tmp/ksocket-myuser/nepomuk-socket (Aucun fichier ou dossier de ce type)"
"/usr/bin/kmail(15566)" Soprano: "Unsupported operation (2)": "Invalid model"
"/usr/bin/kmail(15566)" Soprano: "Unsupported operation (2)": "Invalid model"
"/usr/bin/kmail(15566)" Soprano: "Invalid iterator."
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 2 (X_ChangeWindowAttributes)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 2 (X_ChangeWindowAttributes)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 2 (X_ChangeWindowAttributes)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x1000658
X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x1000658
"/usr/bin/kmail(15566)" Soprano: "Could not connect to server at /tmp/ksocket-myuser/nepomuk-socket (Aucun fichier ou dossier de ce type)"
"/usr/bin/kmail(15566)" Soprano: "Could not connect to server at /tmp/ksocket-myuser/nepomuk-socket (Aucun fichier ou dossier de ce type)"
"/usr/bin/kmail(15566)" Soprano: "Unsupported operation (2)": "Invalid model"
"/usr/bin/kmail(15566)" Soprano: "Unsupported operation (2)": "Invalid model"
"/usr/bin/kmail(15566)" Soprano: "Invalid iterator."
"/usr/bin/kmail(15566)" Soprano: "Could not connect to server at /tmp/ksocket-myuser/nepomuk-socket (Aucun fichier ou dossier de ce type)"
"/usr/bin/kmail(15566)" Soprano: "Could not connect to server at /tmp/ksocket-myuser/nepomuk-socket (Aucun fichier ou dossier de ce type)"
"/usr/bin/kmail(15566)" Soprano: "Unsupported operation (2)": "Invalid model"
"/usr/bin/kmail(15566)" Soprano: "Unsupported operation (2)": "Invalid model"
"/usr/bin/kmail(15566)" Soprano: "Invalid iterator."
kmail2(15566) KMReaderWin::setMessage: void KMReaderWin::setMessage(const Akonadi::Item&, MessageViewer::Viewer::UpdateMode) QSplitter(0x1c79610, name = "splitter2")
kmail2(15566) MailCommon::SendMdnHandler::Private::handleMessages: AKONADI PORT: Disabled code in   void MailCommon::SendMdnHandler::Private::handleMessages()
kmail2(15566) KIO::DataProtocol::DataProtocol:
kmail2(15566) KIO::DataProtocol::get: kio_data@ KIO::DataSlave(0xda8f870) ::get(const KUrl& url)
kmail2(15566) KMKernel::slotProgressItemCompletedOrCanceled: Last resource finished syncing, mail check done
kmail2(15566) KMKernel::instanceStatusChanged: A Resource started to synchronize, starting a mail check.
kmail2(15566) KMKernel::slotProgressItemCompletedOrCanceled: Last resource finished syncing, mail check done
"/usr/bin/kmail(15566)" Soprano: "Could not connect to server at /tmp/ksocket-myuser/nepomuk-socket (Aucun fichier ou dossier de ce type)"
"/usr/bin/kmail(15566)" Soprano: "Could not connect to server at /tmp/ksocket-myuser/nepomuk-socket (Aucun fichier ou dossier de ce type)"
"/usr/bin/kmail(15566)" Soprano: "Unsupported operation (2)": "Invalid model"
"/usr/bin/kmail(15566)" Soprano: "Unsupported operation (2)": "Invalid model"
"/usr/bin/kmail(15566)" Soprano: "Invalid iterator."
"/usr/bin/kmail(15566)" Soprano: "Could not connect to server at /tmp/ksocket-myuser/nepomuk-socket (Aucun fichier ou dossier de ce type)"
"/usr/bin/kmail(15566)" Soprano: "Could not connect to server at /tmp/ksocket-myuser/nepomuk-socket (Aucun fichier ou dossier de ce type)"
"/usr/bin/kmail(15566)" Soprano: "Unsupported operation (2)": "Invalid model"
"/usr/bin/kmail(15566)" Soprano: "Unsupported operation (2)": "Invalid model"
"/usr/bin/kmail(15566)" Soprano: "Invalid iterator.""

Is that helping ?