ISC must be turned off in Ecu Editor under Advanced Settings, to sync throttle bodies on an 08 or newer Busa.
Gen2's have STP's, secondary throttle plates, also controlled by the ecu.
Suzuki dealer will turn off ISC with Suzuki software when they do a
gen2 throttle body sync. Otherwise, you use Ecu Editor, Woolrich, or ECU Unleashed to do this.
Ecu Editor can flash an ecu, and back to stock at any time, and without causing dealer problems.
But apparently Woolrich software(I have no personal experience with Woolrich)permanently changes how the ecu code is read.
Possibly causing dealer Suzuki software or Ecu Editor to not recognize your ecu.
That is what I would look into.
If the bike is running decent, the ecu is fine.
You may/may not be able flash that particular ecu now for whatever reason.