Why doesn't the bounty hunter die in this X-Files episode?

Question

Part of the alien lore in The X-Files is that the alien race can only be killed by using a specific weapon and stabbing them at the base of the neck. The weapon is a sort of stiletto which Agent Mulder originally learns of after finding one hidden in a lamp in his summer home. This happens in the season 3 finale episode "Talitha Cumi".

At the end of that episode, the character commonly referred to as the Alien Bounty Hunter shows up to assassinate Jeremiah Smith, another alien of the shape shifting race who has defected from the conspiracy. A fight ensues and Mulder eventually gets the jump on the bounty hunter and stabs him in the base of the neck with the stiletto and escapes.

In the next episode, the season 4 premiere "Herrenvolk", Scully stops to check the pulse of the bounty hunter who has been lying motionless and presumably dead, with toxic blood oozing from his wound. As she does this, the blood suddenly disappears and the bounty hunter wakes up, pulls the weapon out of his neck, and takes Scully hostage.

So... what just happened? All signs pointed to him being dead, so why did he suddenly come back to life? Did the weapon not work? And why not?

Answer 1

There may be better, more official, sources to answer this, but the X-File fandom wiki poses the following solution:

The bounty hunter pursued Agent Mulder and Jeremiah to a bee husbandry facility in Canada, recovering easily from a failed attempt by Mulder to kill him. It is likely the reason the bounty hunter did not die from the wound was because Mulder didn't remove the gimlet weapon from the body. This stopped the wound from bleeding out, and prevented the bounty hunter from dissolving; or because the stiletto didn't go all the way through the bounty hunter's neck because it went through the back of his suit into his neck.

Just fan theory, of course. We don't know all the particulars about how this weapon works, but it's entirely plausible that Mulder simply used the weapon inefficiently, and therefore failed to actually kill the target. Like someone who's never held a gun in their life trying to shoot a moving target. (Statistics indicate that even trained police officers have around 30% hit rate, even when there's no return fire.)

Answer 2

I disagree with the fan theory stated in Steve-O's answer. This answer is an extension of those comments.

In one of the conversations leading up to the incident, the Samantha-hybrid had warned Mulder that the weapon needed to be targeted in a precise location. Therefore my impression of the event was that Mulder simply did not hit the right area.

This is the same reason why, in Season 6, when Krycek and Spender were assassinating the rebel posing as a Syndicate member, it was Krycek, not Spender, who actually did the stabbing. Krycek is at this point in the show a highly experienced assassin, and for all we know he's been specifically training to do this kind of thing.

As to why the bounty hunter looked dead-ish: the aliens and hybrids still can get hurt. For example, in Season 1, the hybrid Secare was starting to die from his wounds and exhaustion. And in Season 6, both Exley and the bounty hunter got knocked out cold from baseball hits to the head.