At first, the Journal of Facts was scared by the fact it had been unable to prevent Jane from writing it would be destroyed, but thankfully that part didn't get any related illustration and, being written as a new paragraph, the Journal could dismiss it as not related to the story.
Now, it just needed to find a crack into the goddess' mind and… Ah here it is.
Being a 12th dimensional creature, (a.k.a. a goddess) Faith can see and feel things no human can, as silly 4th dimensional being. (Yep 4th, three ‘spatial dimensions’, sometimes called material dimensions, and one for time.) That's what the concept of a being that's a part of someone-else while simultaneously being themselves is so hard to understand, even for humans having an angel.
The same kind of logic apply to feelings. For most humans, friendship and romantic love are mutually exclusive. Not only that, but they tend to see romance as something more than most other kind of love, like it was some sort of ‘upgrade’ or something. And that's why Faith was unwilling to reveal all her feelings for Colin, because he is human, and as such he probably won't be able to become her lover without stopping being her friend.
And that emotional turmoil was all the Journal of Fact needed to be able to manipulate the goddess.
It made Faith cross-out the paragraph about the goddess destroying the evil Journal, and write two time that not even gods could destroy it, to make it definitive. But felling smug, the Journal let its guard down, giving Faith an opportunity to counter-attack.
She wrote the Journal couldn't corrupt or even influence a heart as pure as a god's one, (pure not meaning without feelings nor without doubts) before adding it didn't know Colin had any angel, because he's still a human, indistinguishable from other human unless he use his magic or manifest one of his angels. She also wrote that once this Journal choose an ‘owner’ it couldn't be changed until the current one ceased to be. All this being written two time so it couldn't be changed back, naturally. In fact, like all times things were written two times, the text disappeared, making it so things were always that way for everyone. (Although gods could tel it wasn't true.)
Now that the Journal was neutralized, she gave it back to Colin, asking him to be careful with it, just in case. Sure, she could have used it to change Colin into a god, or at least make him able to become her lover without stopping to be her best friend, but that wouldn't be fair to him. And he is one of the few humans good enough they might ascend to godhood, that's why she gave him Aqua so long ago. All she can do is wait, and hope for the best…