What one needs to understand before drawing that conclusion is that there is such a thing as a body-only resurrection. Such is the case with Metal Shark Player's abilities, in which through illegal DNA resurrection, he calls back the form of a dead Maverick but is in fact controlling said Maverick; the dead Maverick's will is not part of the equation. X, likewise, does the same when he obtains MSP's powers. Also, there's Maverick Hunter X, which leaves the indication that boss revival is a simple matter of "animating the body", as X finds Launch Octopus devoid of personality when they rematch. It's a sharp contrast to the Zero series, in which Neo Arcadian bosses are fully conscious and capable of conversing upon revival.
I'm not sure what the earliest point is that we can say a "lost soul" was called back to the world of the living (barring Sigma which we know is some manner of virus kerfunkery). In Zero's case, the Control Chip survived containing his personality, so in a sense he was not truly dead, rather his brain was simply unplugged. And that's the problem; we're dealing with artificial beings, they can be powered down, dismantled, bodies broken, and as long as their program is physically salvageable, repaired and reactivated just as easily. "Plucking a cyber-elf" would mean we're looking for the point at which their personality program is impossible to recover from their broken body, and the games don't usually go into that level of detail. Case in point: Vile.