In 1863 the trustees attempted to collect rent and damages for use of university facilities from the confederate government. They received no response, and the Union army replaced the confederates in using the college buildings.
On July 21, 1865, the board resolved to prepare a request for payment from the United States government for the use made of university buildings and grounds and the damage done to them during federal occupancy. The War Department appointed a Board of Survey, which estimated the damage to the buildings of the university still standing at $15,000. Based on the report of the Board of Survey, the US quartermaster general offered to repair facilities as long as the expenditures did not exceed $2,227.11. The trustees declined the offer as financially inadequate and condemned the Board of Survey report for not considering the grounds, fencing, and destruction of the gymnasium.
The trustees sought to strengthen the position of the institution by declaring vacant the seats of seven trustees who had fled from the city as the Union troops approached in 1863. The government then offered to pay $3,144.88, which the trustees accepted with the understanding that “it shall not be considered as in full payment.” The government refused to pay unless the trustees accepted the funds as being in full payment. Following a reorganization of the board, the government agreed to pay the $3,144.88 without the requirement that the trustees agree that it was in full payment for damages.
The university, however, never received the money. On November 5, 1870, the trustees employed F. W. Jones as an agent to lobby for passage of a congressional act to appropriate $18,500 as compensation for damages. The bill passed the Senate and the House but was vetoed by President Grant, because “if the precedent is once established that the Government is liable for the ravages of war, the end of demands on the public Treasury cannot be forecast.” He indicated support, however, for a “donation” in the amount of $18,500. The bill was redrafted to provide that payment was “in full compensation for aid given by and on behalf of said university to the Army of the United States in the late rebellion.” This bill passed both houses of Congress and was approved by the president on June 22, 1874. The trustees passed a resolution the same day accepting the funds and releasing the United States government from all claims. F. W. Jones was paid his agreed-upon fee of $3,500.