To be clear about this EMC thing, the EMC option is two things: A "personality card" that plugs into the front of the analyzer (85712D) AND a card that plugs into the card cage inside the analyzer. The personality card is software only, and the internal card provides the quasi-peak detector (QPD) measurement function (aka Option 103) that is specified by regulatory agencies for EMC measurements.
The personality card contains the driver for the QPD card, and various radiated and conducted EMC limit profiles for DUTs as defined by regulatory agencies. It will plot the received emissions vs. the limit lines and indicate pass/fail for each test.
There's a lot of set up to fully utilize this feature (RF-quiet rooms, LISN's, special antennas, etc.). The user manual that Miti posted provides the details on all of this.
There is also a personality card (11946-10004) that contains only the driver for the QPD card, and omits the various automated EMC limit testing provided by the EMC card.
If you have the QPD card and want to use it, you will need either of the above two personality cards. If you already have one of the above two cards loaded, you will lose this functionality if you wipe out the NVRAM and don't have the personality card to reload it. It is possible to reload the QPD driver and most of the EMC personality card without the original personality card, but it is a painful process as Miti can probably attest.
If you don't intend to do any EMC measurements, I actually would not worry about it.
There is one more thing: If the 859xE SA came from the factory with the EMC option, the front glass over the CRT is special. It has a metallic coating on the inside to help reduce emissions from the analyzer itself. If you ever move the QPD card to a different analyzer, move the bezel and special glass too. The bezel has to move too because the special glass is thicker.
Hope this clears it up. If still not clear, please look through the EMC user manual before diving in any further.