I have a pack and go with toolbox parts.  I also have PDM toolbox and with the settings I can not uncheck the "Make this folder the default search location for Toolbox components" option. 

So on the pack and go every file is saved as a part file but the bolt icon is still showing next to the parts that originally came as toolbox parts.  

We ran the sldsetdocprop.exe tool to remove the toolbox property.  The items are still showing as a bolt icon.  I found that if we suppress the part that has the bolt icon and then un-suppress it the bolt icon goes away.  Its a tedious fix just to get this assembly into our PDM server. 

Has any one else came up with a workflow that deals with these issues?

I will be getting updates to this assembly as work is done elsewhere, and don't want to go through these steps again.  On the sending end he has started saving all the toolbox items as parts.