The major deficiency ruling is often referred to as a "refuse to file" in most of the press.
That is a ruling from the FDA that the submitted application is lacking information that makes it impossible for the FDA to render judgment. In other words, there are clinical data missing from the BLA, manufacturing details are missing, etc...
The opportunity for a major deficiency letter rests at ~60 days after the initial BLA submission by the sponsor. For example, IMCL received this "major deficiency" ruling, or a refuse to file.
Once the FDA accepts that it has all the information available to render a judgment, the possibility of a "major deficiency" ruling has passed and you're into the approved / approvable / not approvable scenario.