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Yes, it can throw codes and could go into limp mode as the sensors will be unable to read correctly. How quickly this happens can vary from truck to truck.
Some of the tuners will actually engage the EGR from time to time for that purpose. Not sure about H&S but I believe Spartan does. Each tune varies though, so check with H&S or wait for someone who has one to chime in.
Smotrs is dead on. Without re-installing the DPF/DOC, your truck will go into limp mode which is a safety to prevent damage.
H&S will cycle your EGR when you use the "Easy Tune." Unless you're returning to stock and driving 2-300 miles before re-deleting, I recommend running easy tune every 10,000 miles or so.
Do no try to drive with the PDF. I you have a tuner friendly dealer then you can pull it around the corner and drive it it. It WILL freak out and try to clean a filter that's not there. Another option is to put the DPF back in and run a stock tune. But the dealer will know what you are up to. Be honest with them or find another shop IMO.
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