Nothing will break. Also, why are you running large FFT?
If Prime 95 comes across an error, it stops the worker thread(s) for that core.
You ideally should be running Small FFT to test CPU stability. Make sure to enable Round off Checking under the Advanced menu. Worst case scenario, your computer blue screens and reboots. Most likely though, if you get an error, it will just stop the test on the unstable core.
When you see people say they run Prime 95 for 24 hours to check final overclocks, you think we stay up for 24 hours straight monitoring the test?