Hi Geoige,
I am not sure why or even if they are separated.
My guess: Normally, if a sword is polished, a shirasaya would be made (post polish) so it doesn't get scratched by being placed back into its original Saya. The saya would then (normally) have a tsunagi made to keep the Koshirae together. But everything gets damaged if not looked after. So, if the sword gets rusty and is ruined, then there's a spare Koshirae. Likewise if insects eat the Koshirae, there is a stand-alone sword. Perhaps someone with a large collection passes away and the Shirasaya are separated from the Koshirae and the family mix them up, or sell them separately, not knowing they may be paired. Once parted, it's almost impossible to re pair them.
Koshirae were changed out from time to time as the fashion, mood or even the law dictated, so a Samurai or Daimyo may have had several Koshirae for the one blade or blades (Daisho), depending on what they were up to. Especially during the Edo Period if attending the Castle. For example; they may have changed their 'local' or cultural regional koshirae (Higo, Owari, Satsuma etc) out for a Banzashi Koshirae, more in keeping with the etiquette or even the laws of visiting the Castle - Horn Kashira and rounded Saya on the Wakizashi for example. Perhaps they wanted something more flashy than their 'daily' Koshirae if they were visiting the Saki (Geisha) houses and wanted to show off a bit. Swords were expensive, so it made sense that they may have had several Koshirae for the same pair of swords, to suit different occasions. And that is without even including the wealthy merchants who probably changed Koshirae on their Wakizashi as the fashion, Zodiac year or even the seasons and festivals dictated. Samurai may have done the same.
Lastly, (and this is a wild guess here) collectors may not want the Koshirae - or or the blade - as that ls not the focus of their collection, so they sell (or don't purchase) the other, in order to further fund their hobby..? Or they fall into hard times and have to sell one half to keep afloat? Who knows.
As for pairing them back up, my advice would be nope, and don't even try. Apart from not having the money or resources to do that, it could potentially damage the blade in doing so.
Barrie.