That still doesn't explain what actually happened them though. You also have the problem that all the First Founding chapters probably had records as well (not to mention other organisations), seems a bit complicated that they all lost the relevant data.
They are more or less like Cypher, Farsight, and other 40k mysteries. We can all come up with our own views on what happened to them. Unless GW tells us, we won't know for sure. We can shoot theories around here and pick apart them, but that's about it.
I like to think that the 'Data Missing', 'Data Removed', ect. is just a localized problem. We don't know whose 'library' we are looking at, how reliable it is, and where it is located. I like to think that one Missings Legion is Traitor and the other is Loyalist and the actual 40k Characters know who they are. If I asked, say, Calgar who the Missing Legions are and showed him the chart, he would reply something like "The Sons of Terra are on the East Fringe with us, serving with honor. The Star Strikers are traitors. Latest intel puts them in the Eye."