You bumped a fairly old thread to ask a fairly lame question. Possibly you should try using google better, or just reading about nds homebrew in general, or possibly even reading.
First is to clear up something. Unless it's something like r0mloader.nds, taihen.nds, flashme or another thing along those lines, homebrew will pretty much NEVER do jack shit to your flashcart. Either it works, it doesn't work, it halfway works, or it halfway works and fucks up every file on your microSD.
Also, if you are planning on bumping a not so recent post, at least try to read the fucking thread because if you didn't notice, the thread is talking about MS2 on an acekard ._. ...Despite the fact that there are multiple threads about moonshell2, two or so threads that are well made and pretty much specifically for any and all dealings with moonshell2 as well as an acekard/moonshell2 combination, of which you seemingly missed, I shall help you with your problem.
It works. Google tells me so. I tell me so. My DS that uses it tells me so. EVERY FUCKING PERSON THAT HAS NEVER SAID ANYTHING ABOUT THEIR AK BRICKING BECAUSE OF MS2 TELLS ME SO. All in all, just read a little more, pay a little more attention, and remember that unless it is meant to do something bad or risky, homebrew isn't going to kill your flashcart.