As far as I know, you can't really do anything there about your Journal... I don't think at any time in Amnesia itself had you ever needed to lose pages in your journal, even after the grunts attack you and throw you into the cage. Unless you FC a way to disable your journal perhaps after picking up a note, then later on finding the same note in a similar area to make it look like you dropped it.
Also, what you're talking about (I think) is this:
GetEntityExists(string& asName);
I have never tested it, but I will assume that a name you assign something in the Level Editor is what goes into as a string. This was probably used (unless local/global vars were) when Daniel would pick up parts of a diary (where he would read) and it would determine which of the three you had picked up. Again, just an assumption. Haven't looked at those codes.