A little bit more of the technical side of this (Robyn has probably in-fact explained this elsewhere):
Every Building (or prop) Exemplar includes a Property titled Resource Key Type (abbreviated as RKT) X (where X can be a number from 1 to 5, with each number having a specific meaning). Usually for Buildings the property is RKT 1. The value for this Property is the TGI for the model used for that building.
The problem you are experiencing is caused by process used by creators of especially the earlier custom content, whereby, instead of just creating a new Building Exemplar from a specific model, they would instead create a prop using that model, and then use a blank model for the RKT property in the Building Exemplar. This process was often used (and is still used) where a lot may include multiple buildings, and a content creator wanted to create a Building Exemplar for the entire lot (for example an industrial site). This was no problem as long as the TGI used in the RKT property was the one for the blank model included with the game. However, some creators felt a need to create their own (thus creating a new dependency), while others I suspect just created a nonsense TGI.
If I understand Robyn's solution correctly, one tells the game to disregard the TGI in the RKT property by changing all the numbers to zeros (0), i.e. a null key. The game looks at the null key and just disregards this value, and alleviates the brown boxes that would otherwise occur if the game couldn't resolve the configured TGI (this may not have been understood early on, or may just have been the way to go for this type of lot).
This would be a much faster solution than trying to find the blank model created by the content creator (or someone else's), or going the longer route of just creating a new Building Exemplar directly from the model (if you are relotting the model anyway..., but I understand the impulse to just use the existing Building Exemplar).
BTW, if your lots are working correctly in either of your Plugins folders, did you try scanning with DataNode to see what the lot is actually using?
Hope this hasn't created more confusion. I know it took me while to figure out what was going on back when I first experienced this.