DSO has long been known as a memory card rapist. You should expect that this may happen again if you keep using it, so back up your important data frequently.
I don't know exactly how to recover files from an SD card, but I do know that if you want to try to recover them you shouldn't write anything to the card at all, or the data may be permanantly lost.
Thats good to know, but ATM my Evolution hasn't shown up so I'm running it on my crappy Games'n'Music with it's iffy DLDI drivers and my 2G Kingston and haven't had any corruption problems that I noticed. That is until I tried to upgrade DSOrganize to the 3.11129 version the other day at which point a straight copy would fail as it would say that the CACHE directory was NOT empty. Looking at the directory itself showed it to be read only, and trying to untick that led to it being marked read only again immediately. The directory itself looked empty. I ended up fixing it by running scan disk on the card, fixing filesystem errors, then just blowing away all the DSO files and directories, then trying to install again which worked fine. Had a bunch of lost files, which I am sure were what were supposedly in the recalcitrant directories.
Some people probably won't like that solution, but in my case I've only had a DS for about 2w, and din't have anything importantin DSO yet, so if you KNOW what files are what for DSO I'd imagine that you could save/back those up, re-install then replace the important data files to get back to what you had. I don't know yet, what anything is in DSO file structure yet, but I do know that the web browser seems to be pretty good for a little device(needs bookmarking and/or some integrated way of storing links, if there's one there I've missed it to date), the IRC client is good, and the homebrew db browser nifty(db's a little sparse though).
I NEVER would have noticed the DSO ptoblem, had I not decided to install the updated version AND decided to do a drag-and-drop overwrite upgrade. Another little problem I had was that initiallly I tried it under win2k and my USB subsystem locked the OS HARD(no blue screen, but also zero activity) so I had to reset, which is just as likely the cause of corruption. (I suspect that my win2k problems are related to the various evil copy-protection systems, and virtual disk software that I have installed getting confused that my memory stick is a CDROM that need "protecting" from my nefarious activities. Damned copy protection must die, especially since I can't run The Witcher under win2k because of it. (Works fine as expected under my XP Pro install, but I still prefer win2k. Also finished my DSO updates under XP as I have less software installed under it and almost no games, so no evil copy protection.)
That said, I've got a 3in1 too, and I don't think that the 3in1 had anything to do with your problems. The 3in1 w/o running any sw is a mostly inert hunk of silicon and plastic. The sw used with it, Rudolph's 3in1, integrated, etc. might do bad things, but I'd expect it to corrupt things in it's own directories and not DSO's. In any even Rudolp-h's tool has been running on mine for about a week, and hasn't messed anything up yet.
(Anyways, I'm in this forum looking around as I'm scouting a different type of flash cart(slot 1) backup for my Evolution, but I've got it down to I'll either spring for a M3DS REAL Perfect combo cheap build quality and all, or maybe an R4DS SDHC if it ever comes out plus an EZF IV Lite Deluxe or the ewin expansion pack as I'd rather have DSLinux see 32M(ewin) v. 16M (EZFIV). (want a slot-2 backup as well.) DSLinux doesn't like my GnM with my 2G ATM so I'm just whiling away time awaiting my evo.)
