If it has an aftermarket Fuel Injection programmer (like a dynojet powercommander), it may have lost its programming. Some of the older systems used a serial connection to upload/save FI programming...some newer ones use USB. You would need to identify if you have one - what model it is - then determine what map it needs and upload accordingly.
Sometimes the FI on the bike needs a reset or determine the code being generated. Here is a forum that lists the procedure: