(SPOILERS) The plot twist in which it is revealed that Frank's ancestor purchased the bond from the City of Mayberry in 1861, possibly with (now worthless) Confederate money, therefore making the bond worthless in 1961, bears some scrutiny.
To begin with, even though the banker, the mayor and the rest of the town council quickly turn against Frank in his front yard when they contemplate the year (1861) when the bond was purchased, they are jumping to huge conclusions. It is only mentioned that the bond was purchased in 1861. No month of purchase is mentioned by any of the characters. Confederate money was not issued until April, 1861 and North Carolina did not secede from the Union until May 20, 1861. If, therefore, the bond was purchased sometime between January 1, 1861 and May 19, 1861, Mayberry, North Carolina was still part of the United States. The "Mayberry bond is invalid because it was sold during the Confederacy" argument that Banker Fergus and Mayor Pike make would be invalid.
Second, even if the bond was purchased on or after May 20, 1861 (the date North Carolina declared its independence from the United States), it is never determined in this episode exactly what kind of money was used to purchase the bond. Even after North Carolina joined the Confederacy, Frank's ancestor could have paid in gold or even in state money. In 1861, there was no Federal Reserve issuing a national currency as we have today. Individual states and banks issued their own unique paper money, which was recognized, honored and accepted based on the reputation of the issuer. Certain states, particularly the Northern ones, continued to issue their own bank notes until 1935, well after the Civil War ended. In other words, Frank's bond could easily have been purchased with some form of currency other than Confederate money.
Finally, even if Frank's bond was purchased with Confederate money, if it was purchased on or after May 20, 1861, then Mayberry, North Carolina was part of the Confederacy at that time. The business arrangement/agreement with the bond was made between Frank's ancestor and The Town of Mayberry, not Frank's ancestor and The Confederate States of America. Regardless of moving in and out of the Confederacy, the Town of Mayberry made a business contract/arrangement in good faith with Frank's ancestor and took his money in payment for the same. Therefore, logic would dictate that they make good on it, no matter what the political affiliation of the town is or how much time has elapsed (and Andy points out there is no expiration date listed on the bond).