long story short, My motor took a dump and I had to replace the bottom block. Having the car tuned on an apexi vtec controller, I unplug it before I started the motor thinking that the settings are not going to be good since this is a different motor (rebuilt). The motor now is making noise and can't hold idle. I was told that by unplugging the vtec controller, I lost all data. Is this true? the battery have been unplug for over a few days. shouldn't the OEM ecu reset itself and run on stock setting when I plug back the battery? the vtec controller is still unplug.

 

You can't just unplug the controller, since the controller intercepts the MAP and VTEC wires (and maybe more). You either need to unwire the controller, or just plug it back in, and zero out all the fuel corrections. However, if you only swapped out the bottom end, then the original tune is probably fine.