Grasshopper library conflicts

Hi Guys,

I am using grasshopper with a batch file to launch the file in Rhino and grasshopper.

The process works like this:
An external process completes operations on a file > Rhino opens a said file with grasshopper

The only issue that I am experiencing is that sometimes Iterations of rhino and grasshopper launch at the same time. When this happens one iteration will often not be able to find grasshopper libraries (I am assuming because they are being called by the other iteration)

Is there any way around this. Can I internalise grasshopper plugins into the file rather than a common directory?

Any help on this would be greatly appreciated!