No harm comes to body from doing Mitzvos. This is a fundamental tenet of emunah and worrying about harm coming from doing a mitzvah especially one like oneg Shabbos demonstrates a serious lack of emunah.
In Israel the cuts of meat are different, and while you can get true flanken from Chofetz Chaim, I believe you can only get it frozen. There is nothing better than fresh meat in Chulent.
I have found the best meat to use to be what they call here “Asado”. It is #9. It comes in two versions with the bone (short rib bones I believe) and without them. While not exactly the same cut it basically is flanken. I like the version with the bone since I think it adds good flavor. The only mehadrin fresh version I have found has Rav Machpud’s hashgacha in the bacharein shuk off Yechezkial/Rabbanu Gershom. (They also have it in Rav Rubin but it’s frozen.)
Aside from that, the most important thing to do is too is the keep a low low flame the whole time. If you use a Crockpot also keep it low and raise it up before on Shabbos with a ball of foil on the heat element part (this is a halachic requirement but also keeps the cholent from burning).
Also a Rebbe once told me Carrots don’t belong in Chulent!
Finally, doesn’t hurt to go for a jog/swim/basketball game Motzei Shabbos before sitting down for the Malavah Malka… but never ever compromise Oneg Shabbos by not eating meat chulent!