Following thermal cycling, reaction volume has evaporated from some of the wells of my qPCR assay plate. What should I do?

Make a note of those wells that show signs of evaporation, in order to qualify the data calculated for those wells. To insure that evaporation does not occur in the future, be sure to carefully and completely seal the qPCR assay plate with fresh optical thin-wall 8-cap strips or adhesive optical film before the plate is placed into your thermal cycler. In addition, refer to your instrument's user's manual to determine if the thermal cycler manufacturer recommends the use of a compression pad during the run.