Okay despite having a bit of a struggle for a while I DID find a solution, which I'm posting here for those with the problem in the future.
Why the solution is so limited to this one specific method I do not know, but here we go:
1. Navigate to the composition that is missing Layers
2. In the Project View, locate the source files that you want to use to replace the placeholders with. (I did eventually find them, they were not were I expected them to be but that's my bad)
3. In the composition view Make SURE to left click and select/highlight the placeholder layer that you would like to replace
4. Then left click and hold, then drag the source file/image/footage whatever from the Project view into the composition timeline area and hover it over timeline area, specifically over the timeline bar of that (HIGHLIGHTED!) layer. (If you didn't select the layer in step #3 this is not gonna work)
5. While still holding left click and hovering, then hold the ALT key
6. Release the left mouse button.
7. This should force your source file into the layer, and if it's the same source file as what was there previously, it should fit in perfectly and go back to the way you want it.
I don't pretend to understand After Effects, I just use it.
We appreciate you dropping back by with your solution RyanC. Thanks!