Hello Christian,
Do you get the core dump even when creating a brand new project based on the hello_world template? If so, your workspace may be corrupted. First, check that all your source files are stored in a safe place. Then delete your workspace under <Nios_II_Install_Dir>\kits\nios2\bin\eclipse. Uninstall Nios II, then reinstall Nios II. Create a new hello_world project, and build it to see if the problem goes away. You first may want to check the .log file located in the .metadata directory under this workspace directory, as more details about the core dump may have been recorded here.