When I have two thorns with the same name in different arrangements, e.g. EinsteinEvolve/GRHydro and Zelmani/GRHydro, and then modify my thorn list (which contains one of these) to instead contain the other, Cactus has strange build problems. The root of the problem seems to be that Cactus does not recognise that these are different thorns with different source files, and e.g. the dependency information is not updated. This leads to strange build problems that force me to delete the build directories for GRHydro manually after switching.
One way out could be to include the arrangement name when constructing the build directory name, or to remember the arrangement name and to delete the build directory when the arrangement name changes.