Just to clarify: was there data that you know was in the Codex before, but isn't in there now? If so, that's a bug. Or is it simply that you went exploring some time ago and were hoping that the Codex would have recorded all your old exploration finds?
First, the Codex does not include anything you discovered before the introduction of the Codex. So if you visited Sag A* back before 3.0 came in, and you were hoping the Codex would have remembered and recorded that you had visited Sag A*, too bad - it doesn't. If you want "Supermassive Black Hole" included in your list of discovered star types in the Galactic Centre Region, you'll have to pay another visit.
Second, the Codex is not a logbook that records every single discovery you've ever made. It only records one of each object class, per galactic region.
Suppose you made an exploration voyage (after the Codex was introduced) to visit Sag A*, Colonia, and then back to the bubble - the basic Tourist Triangle. Suppose you discovered twenty Earth-like worlds on that voyage. The Codex will not record all twenty worlds. Rather, it will record the first one that you discovered in the Inner Orion Spur, the first in the Inner Scutum-Centaurus Arm, the first in the Norma Expanse, and so on, for each of the seven Galactic Regions that you pass though while flying the Triangle. So only those seven worlds will appear in your Codex.
In short, the Codex is more a "trainspotter's guide", telling you the different kinds of things which you (and other commanders) have found in each region. It's not a detailed list of everything that has been found.