Do NOT delete the .CR2 files. The CR2HDR.exe has been improved many times in the past so it will most probably get improved again. You may need to process your .CR2 files again...
+1 - that's one of the main drawbacks of dual_iso, it's a lossy conversion cr2->dng and as you will want to keep the original cr2 around there's double the storage space vs. a normal. shot. Only use dual_iso if you know the dynamic range of the sensor has been maxed out (look at the raw histogram or use ettr with dual_iso link).
I don't know how you guys do it, but it seems like one HAS to physically copy the CR2 files from camera/SD/CF to the folder containing CR2HDR.exec anyway in order for it to convert. I've been just keeping the original CR2 files in my usual folders, just deleting the copied CR2 files from CR2HDR folder after processing.
So far in my testing, it does not seem like dual iso will be necessary for my usual shooting situations, only when I encounter near-ridiculous situations. But it's good to have.
Do you guys have the auto ETTR linked to dual iso when you shoot?
ML's auto ETTR does not seem to be producing photo's with histogram moved all the way right for some reason, even if I have it turned on all the time, and the exposure seems to differ even if I shoot the same scene multiple times with focus point on same object.
Also, if I set auto ETTR to trigger with "Set" button, can "Set" be pressed to achieve ETTR BEFORE auto-focus is achieved, or does AF have to lock before ETTR can happen with trigger button?