Now you're asking the right question, and I don't have the answer. I think at that point they had concluded enough about the players to know that there was a serious eligibility concern and did not want them participating from that point forward until it was cleared up.
This would be similar to when Auburn declared Cam Newton to be ineligible per concerns, presented the findings to the NCAA, and then had him reinstated. Your standard operating procedure in compliance is that as soon as you become aware of an eligibility concern you are to IMMEDIATELY report it and declare the player ineligible until the status is cleared up one way or another.
Towards specifics... the competing theories are:
1. The players got held out on the 15th per SOP outlined above, they know or believe they will be reinstated, and it is just a matter of time. This could apply to any or all of them. The logical flaws to this theory mostly have to do with timing, but the supporting logic is if they knew they were toast they already would've transferred or started the transfer process. So somehow, somewhere there is something holding them put.
2. The players got held out on the 15th because that's when their cases were closed, and their fate is still yet to be determined by the honor code committee, etc. There are no logical flaws in this theory, but that doesn't mean it's correct.
3. They're all already toast and Notre Dame is simply slow playing the news because there are other parts of the investigation still ongoing and they want to release all of the final findings at once instead of piecemeal. They know that they're gone so they are obligated to hold them out at this point. The logical flaw with this theory has to do with allowing them to stay in school if they're already 100% toast... classes start soon and someone should be able to know really quick whether or not they're ACTIVELY enrolled. However, the Sykes debacle shows us ND doesn't give a shit about being retroactive.
Each one of your options could be true or false with no logical inconsistencies if you add an option to your matrix for each of the four to be guilty or innocent, independent of each other, and/or if you deal with varying degrees of innocence of each player.
Sub categories come in for players who could take a ding and still maintain eligibility, versus those that were close to the edge and couldn't. The possibilities of this thing have nearly infinite variables, so much so that we cannot expect any rumor either way to truthfully encompass the whole of the situation.
Let alone figure that graduated players did much worse. (Or players from another sport.)
Let alone figure that a deal was being worked for the group, or that the severity of each players punishment is dependent on the silence of the others or all players.
And so on.
When you apply Occam's Razor to this situation, the simplest situation you get is that bunches of people bent the rule of editing versus writing. Everything may come down to how the administration wants to use this as a lesson forward for all students. Someone may be taking the time to think this through.
For example, if SuzieQ, overstepped her editorial bounds by some clear degree while helping with my paper, we (both the administration, my lawyer, and parents) may want to know how common that was before we make a ruling (or accept a deal). Would someone have an appeal, either within the Honor System or legally if one could show what he had done was common practice, or had occurred many other times without any issue?