I suspect you won't find a definitive answer on the fate of those two particular 747's for the following reasons.
The Stratolaunch project is likely still actively using the parts from those planes, so there's no need to dispose of them yet.
747 parts are becoming quite commonplace and their value in the parts market continues to decline.
So that's a bit of a killjoy answer, for which I apologize. Aeronautics is a wonderful field for generating compelling, romantic ideals that appeal to our dreams. The thought of a plane (or two) being used for historic progress and then just being parted out is frankly somewhat depressing.
But when we look at the project management behind an engineering project like the Stratolaunch, the numbers become pretty telling.
This Bloomberg article details how the 747-400 is increasingly being sold off by various airlines.
Now, ten-year-old passenger 747-400s are worth a record-low $36 million, about 10 percent less than similarly aged planes last year, according to London-based aviation consultancy Ascend, as carriers seek more fuel-efficient models. There’s even little interest in converting the passenger jets into air freighters because of a slump in air cargo demand.
Some 48 of the humpbacked passenger 747-400s worldwide have also been placed in storage, according to Ascend. The onetime “Queen of the Skies” has been shunned in favor of Boeing’s smaller 777 widebody (which has two fewer engines sucking fuel) or Airbus’s mammoth A380 double-decker. “There’s not a lot of demand for the 747,” says Paul Sheridan, Ascend’s head of consultancy Asia. “They’re mostly being broken up for parts.”
And this Aviation Week article highlights how 747-400s are increasingly being sold off for parts as it's more cost-effective to sell them than to continue operating them.
with airfield space often at a premium, airliners get withdrawn, re-cycled and chopped up in a much smaller timeframe. ...
The airline can recoup more money selling the aircraft than operating it for several more years before it might otherwise have retired.
Likewise, this NPR article piles on the bad news for the 747-400.
Boeing has scaled back production to only one and a half new 747s per month. Aviation consultant Ernest Arvai expects the company to keep the line running just long enough to replace Air Force One.
To draw that together:
We have a number of elements pointing us towards the fact that 747s and their associated parts are depreciating assets that are possibly depreciating faster than traditional valuations would have accounted for. Depreciating assets receive proportionately less attention as their value continues to decline.
Stratolaunch is well funded and is focused on pushing the edges of space exploration technology. While they may be concerned about how to wind down operations once they're done, I tend to doubt it. Nor are they likely worried about maximizing resale value of the 747-400 parts due to their current funding levels. I suspect they are more focused on how to solve the problems they set out to tackle than they are on "afterwards."
So we have parts whose value is approaching that of salvage only and a company focused on broader objects without much need to optimize short-term economic factors. From the projects I've been involved with, that translates into those two 747-400s becoming a footnote in the company's history; a footnote that the majority of us will never find out about how it ended.
