Altera does not recommend using checksums as a means of uniquely representing a pattern in a device. Altera recommends using a verify operation to confirm that a device has been programmed with the correct pattern.
The Joint Test Action Group (JTAG) IEEE 1149.1 specification also provides a better mechanism for providing a unique signature for the pattern, called the USERCODE instruction. APEXTM 20K, APEX 20KE, ACEXTM 1K, FLEX® 10K, FLEX 10KA, FLEX 10KE, MAX® 7000AE, MAX 7000B, MAX 3000A, and EPC devices support the optional USERCODE instruction.