I believe it was money-related: SFB took a huge hit financially when War Memorial Opera House was updated for seismic improvements, and the company had to perform in two less-than-1000-seat venues (one in SOMA and one at the Exploratorium), except for a season-closing program at Zellerbach ("Swan Lake"). It was closed for 18 months, re-opening in 1997.
Fast forward just a few years (2000-2003) and the Seattle Opera House went through the same process (and, as long as the building was being torn up, included an upgrade), and although Russell and Stowell had been extremely conservative fiscally, PNB was left with a mega-deficit (and almost now endowment), losing audience and donors in the years they had to perform in a hockey rink, where the side seats were permanently affixed and pointing towards where the ice would be, not the stage. They stayed a couple of extra years after their original retirement date to put the company back on solid financial footing.
I forgot about the SF retrofit construction - what you are saying about the construction costs, and the resulting lower ticket sales for these two companies does explain a lot. But how to get companies to do exchange tours as part of their regular programs? And, where possible, extend the seasons somewhat to accommodate everyone's needs?