I seem to have found something that is consistently causing me problems with orphaned activities. I have already solved my problem above as I mentioned but I happen to have noticed that I re-created my problem before when I was changing the color scheme of the toggle colors in Collapsed Topics.
Let me explain more. My initial problem on this thread was that my lectures were becoming orphaned and I wasn't sure why. I initially was just changing the colors when my problem occurred. I have now confirmed why exactly. I use Photoshop to find color harmonies and what I did exactly was copy the color code (html) and paste it into the color code for Collapsed Topics. The second time that I did this, my lectures became orphaned again. Therefore, I believe one of two things. Either this is an error that is caused by code or I myself have incorrectly changed the color code (I mean that to make a simple edit like this, I don't know if I have to go into Maintenance Mode or some other Moodle option).
Either way, I have since replicated this problem and wanted to bring it to your attention because I feel that this is an error of some sort. I don't know if others will have this problem or not.
The one possible reason why this may happen is because we add more lecture topics by using the plus and minus symbols at the bottom of our course to add lectures. This is how we got up to 87 topics. Whether or not that is a problem, we are not aware of it.
Anyway, this isn't a problem we are having, I just wanted to let you know more precisely what our problem is and bring it to your attention.