If I recall correctly, Intel tried a few years ago to sell a system-on-chip combining an Atom CPU with a FPGA from Altera. I believe it didn't work very well, especially with regards to communication and synchronization between the two cores.
It didn't work very well, but there is a good reason: Nobody wanted a slow and comparatively low performance chip paired with a small FPGA connected via a (slow) PCI-express connect. There are hundreds of big FPGA boards with PCIe connectors that can be tied to big CPUs already. It was a non-product from the get-go.
