I got it...   Reason was simply my pi2. It was completly unstable, crashing often, no chance with any overclocking.   I exchanged it. With the same SD Cards the new one runs perfect, no more destroyed file systems. Even with overclocking.   Sometimes if Goldeneye N64 freezes i just pull the power cable and it boots up fine.   So i had only bad luck and got first a pi2 which had bad components. The new one is rock stable.

Look this wiki to have more informations about a dual/triple-boot setup : https://github.com/digitalLumberjack/recalbox-os/wiki/Setup-a-dual-boot-raspbian-recalboxOS-(EN)