It appears that there is a misunderstanding somewhere. Most ("most") IR signals are not NEC, just as most vehicles are not airplanes. If a signal is not NEC, say it is RC5, there is no way to convert it to NEC, just as you cannot convert an automobile into an airplane.

IrScrutinizer will recognize NEC signals as such, if it is recognized as something else (say RC5), it is clearly not NEC. If it is not recognized at all, it is likely somehow fawlty read. In rare cases, it may be a protocol that IrScrutinizer does not know yet.