I'm currently using blender 2.91.0
I was wrapping the UV's of the different objects of my mesh, and in the middle of the process had to apply the scale to some objects so the UVs were sized correctly. After loading my mesh again, the objects that were not at (1, 1, 1) scale (and that I did apply scale to) were all much smaller than normal, and with the scale not applied.
I rolled back to a previous version of my mesh to try replicate the issue, and isolate it to apply scale only. I have the size and scale parameters of the belt object open as an example of the original size. The Horn, Teeth, and Body are all at (1, 1, 1) scale, while the armor and clothing have all different scales. This is the example:
The affected objects have an unnaplied multiresolution modifier only. I checked for Delta Transform and none of those objects has it. What is happening here?