Configuration memory cells in an integrated circuit (IC) may be corrupted by cosmic radiation and other sources, causing improper operation of the IC. Reliability of an IC is improved by refreshing subsets, such as frames, of the configuration data according to a schedule that has one subset being refreshed more frequently than another subset. For each subset of the configuration data, a respective indicator is determined that indicates whether a subset of configuration memory of the IC requires refreshing with the subset of configuration data. The indicator may be a probability that corruption of the subset of configuration memory results in improper operation. A schedule for refreshing the subsets of configuration memory is generated from the indicators. The subsets of configuration memory are refreshed according to the schedule, with one subset being refreshed more frequently than another subset.