Some tools are available in the Ops Center Land Manager, like merge and split, see the video. 
Actually the guy creating the video uses GeoPard (his review is on the website landing page).
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It looks like our GeoPard could be the right tool for this case.

I'd suggest having "dirty copies" of boundaries in GP (we don't charge for intersects, calculate only geospatial Union of fields, so it could be cheap), run calculations, and send only what you need for farm operations in the Ops center.

What is supported:
- Boundary management / sync with John Deere (in and out)
- Recalculation of yield / application data per new boundary
- Sending of yield / application data recalculated per new boundary in Ops center
- Automated smart processing of imagery per edited boundary
- If needed per polygon trial analysis 

Tutorials are here: GP-JD integration (and pages under it).