Most vehicle computers can be reflashed or reprogramed after 1996. Normally this is done by the dealer. The reflash usually "fixes" software type bugs that affect the vehicles performance ie. better transmission shifting, incorrect calibrations, check engine light problems, etc... The tech involved in the reflash has no control or imput in the actual program or download, ie cannot manipulate or change settings. The tech simply facilitates the download just like updating software on your desktop. The only "do it yourself" involves buying an aftermarket SAE J2534 reprogrammer and buying a subscription at the dealer's website. The tool is readily available and used in conjunction with a laptop. The SAE J2534 is the governments specs for the tool, and assurance of the tools compliance. Subscription prices vary by manufacturer. It is very impracticle for an inexperienced user. There are alot of performance "reflash" tools that you can buy especially for trucks. These are NOT the same as the J2534. These are generally not endorsed by the manufacturer, and do not utilize the manufacturer's updates. They simply "overwrite" the current calibration of the vehicles pcm with a performance calibration which may or may not pass emissions. Some will "save" the factory calibration so that you can return to what you started with. Some will also allow you to clear codes and check data. Results are mixed and difficult to prove.
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