I see what you mean, I thought you meant if the original chd was converted using v3 and I was now extracting it with the current chdman that might produce problems.
Should the CRC32 of the generated bin file match the one from the original set? I'm guessing it should, so if anyone has linlhutz's pack and could double check the CRCs for me that would be great and the only way for me to know that all went well. It's only a handful of games that I need so I can convert those and send the CRCs of the generated bin files for confirmation.
I always prefer bin+cue over chds, on top of everything you can also burn them to physical media