Most FI systems can compensate for the changes made by simply installing a different pipe, unless the airflow characteristics are seriosuly changed. However, while the FI map may cover the range of conditions caused by a new pipe, it will be doing it outside the optimum settings of the FI system. So the bike will run, it just won't be perfect
Enter goodies like the Power Commander...
What the PC's do is insert themselves between the sensors and the FI system. You use a map on the PC and it sends fake data to the FI system to trick it basically. For some bikes, with specific modificatins, you can download maps from the PC website or other places. However, even an identical bike to yours with the same mods is not really an exact match, but often the maps are good enough that it won't matter.
If you really want things done right ($$), then you take the bike to a shop with a dyno. BEFORE you have the pipe installed, you have them run a baseline dyno run to see what the stock perfomance numbers are for your bike. Then you install the pipe, air filter, or whatever and run another dyno run to tweak the air fuel ratio at different thottle positions and loads. This yields a custom map for the PC that is then used to feed data into the map of the FI systems. Ideally, you will then have an optimum air/fuel mixture for all possible conditions. This is confirmed during the dyno tuning by the use of a gas analyzer stuck in the exhaust of the engine while you are doing the dyno runs. It's really quite fun...
The result of the time and expense is maybe a few more HP and Ft-Lbs of Torque and a smoother running bike.
On carbed bikes, there are little dohickies in the carbs that control the amount of fuel that sprays into the air moving through the carb. These are called "jets". Rejetting a carb means adjusting the jets to accomodate a change in the airflow characteristics of the engine, as might be caused by a new pipe, air filter or other mods. It's easier and cheaper to do than remapping an FI system, but it is also not as controllable or precise. It is more of a black art...
Adios,