Doing a second "Convert to DNG" on another batch of photo with different settings will affect the first task already in progress (it will inherit the settings of the second).
Folder 1 with Raw photo's. Do "Convert to DNG...", start converting
Folder 2 with Raw photo's. Do "Convert to DNG..." but with "lossy compression (new Lightroom 4 feature).
As soon as Task 2 starts, it will affect Task 1 (already in progress): It will start doing "lossy compression" on the raw's that where not converted yet.
I observed the difference in file size by accident. Luckily I had a backup.