Animation Didn't Function, Then All Animations Were Deleted

Buckle in folks, this is a long one.

Alright, so my team and I have been working on four extended projects (all inter-related) with many sub-projects for a few months now. Each of these sub-projects are created from one of three template files, depending on the content of the sub-project. So to clarify, we have many Storyline files that all were created from one of these three templates. All of the templates are essentially the same, and are exactly the same in relation to the issue at hand.

A bit of backstory. While we were creating these templates, we set up a custom Try Again layer. It had an entrance animation (fly in) and an exit animation (fly out). While we were testing it, we didn't really think anything of the fact that when we closed the layer (triggered by clicking a button), the exit animation didn't play. To clarify, the fact that it doesn't/didn't play isn't an issue, it's hardly noticeable anyway. But, because we didn't notice that it wasn't playing, we forgot the animation was even on the layer; so, the animation stayed. The layer's timeline is just over 12 seconds long.

For the first three extended projects, we didn't run into any issue. Even if our Try Again layer was left up for a few minutes, nothing happened; basically, the animation wasn't occurring. However, on the fourth extended project, all of a sudden a few Try Again layers, when left up for the approximate 12 seconds, would animate and fly out, thereby leaving the user with no way to return to the screen except by refreshing the page. To clarify, the fact that the animation is now occurring isn't the issue, as we are aware this is how it is supposed to function. The issue is that the animation wasn't functioning to begin with, and even when it started functioning again it only happened on a few select slides.

We've found the connection between these slides to be that the Try Again layer was pasted from an Object slide (which contains all of the elements we use throughout our projects) to a slide that held multiple hotspots. From there, that Try Again layer was then pasted onto multiple other slides. Those slides are the ones where we saw the animation appearing once again. 

So, the first question is: Why weren't the animations playing? And what was it about those particular slides (with multiple hotspots) that started to get it to play? Please note that on the first three extended projects, these same Try Again layers were also pasted to slides with multiple hotspots, however the animation was still not playing.

If you've made it this far, thank you, and I'm sorry but there's still more to this story.

Once we realized that this animation would cause the screen to become unusable for our users, we started removing the animation from only the slides where the animation would play. At this point, we hadn't realized that the issue was that most of the animations weren't playing, not that they were. So, we removed those select few animations and went about our merry way, continuing to put the projects into review and moving them along. It was at this point that we were going to submit an Articulate Support Case or make a post in the Community about the issue we thought was occurring so we could know how to fix it for the future. However, in putting together the information, it dawned on us that those select few slides with the animation that was playing were the ones that were functioning correctly. After making this realization, we decided it would be best to go through and remove the animation from every Try Again layer in every sub-project of each of the four projects. But when we opened the projects, all of the animations were gone. Even for projects we hadn't opened, the animations just... weren't on the Try Again layer anymore.

So our second question is: Why did all of the animations disappear?

Off of that question, unfortunately I don't have a Storyline file that I can attach because, as I stated, all of the animations aren't there anymore. Whenever we add an animation back on, it functions as it is supposed to. Given that, if you have any questions I will try to answer! As far as we were able to tell (and we did a lot of digging) there was no perceivable difference between any of the files, and they were constructed the same way each time.