Question:
What happened to the University College of San Francisco? In 1859, the Reverend George Burrowes founded University College in San Francisco. Confusingly, it was also known as City College.
Short Answer:
Regarding this blurb in your research:
In 1864 there was a "decree entered in favor of plaintiff" in The President and Board of Trustees of University College v. The Trustees of the City College of San Francisco. (In 1935 the city created a Junior College on another site which became the modern City College of San Francisco.)
What I found was the Presbyterian Synod of the Pacific set up the original City College in San Francisco. The Board of Directors of that City College, not the City of San Francisco then moved the City College out of San Francisco to San Anselmo in 1892. Where it still remains.
How I found it:
I started by looking for Reverend George Burrowes grave site to see what it would tell me and found this.
George Burrowes, D.D. Apr 3, 1811 - Apr 19 1894 (aged 83)
A third name ever to be held in remembrance as that as one of the founders of the San Francisco Theological Seminary is the name of Rev. Dr. George Burrowes. He began his services as Professor of the Hebrew Language and Literature with the first term of the Seminary, and for almost a quarter of a century he continued his remarkable expositions of Scripture and in the manifestation of a beautiful Christian life.
Then I searched for San Francisco Theological Seminary and found this
In 1871, SFTS (San Francisco Theological Seminary.) began with four professors and four students meeting for instruction at the Presbyterian City College located in what now is Union Square. Six years later, the seminary moved to its own building next to the City College building on Haight Street.
Then I searched for Presbyterian City College San Fransisco and found this.
Union Square, San Francisco, CA
The San Francisco Theological Seminary described its own origins: "Presbyterians in the Bay Area in the mid 19th century, determined to establish Presbyterian institutions of learning in the West, found a leader in pastor, preacher, and scholar, William Anderson Scott. Largely under his direction, two schools were started in the churches he served in San Francisco. The first was a Presbyterian college opened in 1861 in Calvary Church. The second, and more long lived, was San Francisco Theological Seminary. When in 1871 the Synod of the Pacific charged a newly appointed Board of Directors with 'organizing a theological seminary such as the present wants and future interests of this coast demand,' four professors and four students began meeting for instruction at the Presbyterian City College located in what now is Union Square. Six years later, the Seminary moved to its own building next to the City College building on Haight Street." (See "SFTS History,"Accessed 02/16/2012.) The school moved to another location in 1877 on Haight Street, and then in 1892 to a spacious and secluded new campus in San Anselmo, CA.
I then searched for "city college" San Anselmo, CA and found it.