I have been running qPCR to quantify pDNA within lysed cell pellets. I had noticed that the pDNA titers had changed when I ran dilutions of the lysates on qPCR a few days after the first run. These lysates were stored at -20 degrees. The change in titers depended on the sample being run. I've experienced an increase in titers as well as a decrease upon reruns with not much consistency other than samples that increased titer continued to do so and samples that decreased titers continued to do so.