I searched the forum Topic Threads, ‘moving between layer’ and 'moving layer', but results not related.

I'm editing my third saved copy/version of an Inkscape file, cleaning it up a bit--making sure there are no extraneous objects, cleaning up the layers--then I found this very strange behavior.

Moving a layer from one position in the hierarchy of layers to another, the drawing was moved and scaled up something like 200% as you can see in the example on the left. I tried moving by copy, then paste-in-place, but the moved object changed proportion.

Well. All of this scaling is very unexpected and very bad for my use. I created a "drawing template" in Inkscape and then made a 3D print. Super fun. After each print I tested the template and then made adjustments to the layout and template opening so it would better accommodate the ball point pen I wanted to use. The first three versions worked fine, but the last version does not produce a good print file. I'm troubleshooting that, when I discovered this bizare scale issue. Obviously, if I'm incrementally making changes based on the current file, then any unintentional/silent scaling or change of proportion is undermining the process.

I'm a noob at Inkscape. Maybe it's doing something very reasonable. To create the template design, each figure was created once. Then I duplicated and scaled the figure up. This gave me two sizes for each figure as you can see in the example on the right. Is this scaling somehow coded to the layers? Does changing the layer arrangements somehow apply the scaling again? Is there a step to flatten the image and reset all of these phantom scaling to 100%??

1. Describe your OS (your computer's Operating System: Mac/Windows/Linux/etc. & version).
2. Describe if Inkscape was newly installed, or upgraded from an earlier version.
3. Describe the version of Inkscape and the installer you used (the file you downloaded from the web: .msi/.exe/.zip/appimage/other, PPA/Snap/Flatpak, dmg/other ). 
4. Describe any special hardware being used, like tablet/stylus, external drives or multiple monitors.
5. Describe any helper/assistive programs or keyboard modifiers (macros, languages, etc.).

Bonus points, if you:

• Attach* a screenshot of the issue.
• Attach* an example SVG file that has the issue.

It is likely there are layers with scaling transforms, and moving layers into another compounds the transforms.

"It is likely there are layers with scaling transforms, and moving layers into another compounds the transforms."

How do I verify if this is the case?

Is there a way to "apply" all transforms and "commit" to what's evidently visible and make everything on equal footing-100%?

You can check it in xml editor. It would be simplier to share the svg file (paperclip icon) for inspection.