So yesterday was final testing, everything came together with all the solutions that we made these past few weeks.
Manuel process was working fine, all the documents from the first drop off library seemed to route well to the second drop off library on the sub site. After doing the PowerShell command, all the 1000 test documents were pushed into the first drop off library on the root web. Ok this seemed to work fine, now it was time for the content processing timer job of SharePoint to do its magic. After the work of the timer job everything seemed to be in order, “seemed” being the key word here.
All the documents were indeed routed to the drop off library of the sub site but my event handler that was placed on “ItemAdded” on the dropoff library wasn’t trigged. Only logical conclusion was that the content processing timer job does a disable event triggering and an enable event triggering while it’s doing its job on routing the documents.
The solution was instead of an event handler on “ItemAdded”, creating a workflow that simple did the same thing, only execute the code. Keep in mind that you have an additional tracking system with the workflow history mechanism (thanks tom for the help :-)).