Publishing an existing workflow step after adding libs using ilmerge (xrmtoolkit)

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CRM

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Hi all,
I created a WokflowAction for our CRM and published the assembly.
After a while I was forced to update the WorkflowAction to support some kind of serialization using NEWTONSOFT.JSON library which I added using ILMerge and the XRMToolkit.

Now I can not update the assembly on the CRM system without getting "missing type" exceptions.

using the commandline ILMerge successfuly creates the assembly, I checked it and it looks fine.
I just can not deploy it, neither with XRMToolKit nor with the Plugin Registration tool (missing types).

I did some research and so far the only solution I came across was to remove referenced workflows, then remove the assembly and deploy it "fresh".

Is that true? Or is there an other option I could try...
Removing all workflows would be quite a hassle...

Any ideas are kindly appreciated,
cheers
Andy

What I have tried:

I tried to publish the commandline generated assembly via PluginRegistrationTool and XRMToolkit
I checked the ILMerge generated Assembly with decompilers and my testenvironment, works like a charm.