Yup, you can definitely use a Flashpaq to pull DTC codes and clear them.
Ok. I know I can read the manual but it is not in front of me but I assume you plug it in and click on the DTC option and it wont impact the settings you already have in place?
To be honest I'm not 100% sure but I drove with mine cracked for about two months and never hurt anything but that's not to say it couldn't. I don't think it would matter but I'm no expert.