I'd like to concentrate my eluted plasmid DNA by heating it up in a thermocyler. The plasmid is eluted in water, and I don't have access to a speedvac right now.
I did it for a Ti plasmid purified from E.coli. I transformed the resuspended plasmid both in E.coli and A.tumefaciens afterwards and colonies grew and also the tobacco plants infiltrated with plasmid transformed agro expressed the correct proteins. I didn't want to heat at too high temperature because I was worried about the plasmid integrity and I did it in a thermometer not in a thermocycler as thermocycler controls the added heat according to a volume. During the water evaporation the volume of your plasmid will change and therefore, the temperature will be increasing over time.
So long as the temperature is below the melting temperature of the DNA and you don't have lots of contaminants in the solution that could damage the DNA then it should not be an issue. After all, many thermophiles live at elevated temperature and their DNA is fine.