Well, it depends on the what libraries you are renaming folders in.

You can safely move files within each of these library folders:

Camera
Character
Face
Hair
Hand
Light
Materials
Pose
Props

Never rename folders inside the Geometries or Textures folders, or any of the additional morph type folders that appear directly inside the "Libraries" folder. 

I'll give you an example:

Let's say I have a package that I want to install that includes a top, pants, skirt, hat, boots, purse and hand poses for the purse.

Now lets say that when I unzipped the zip file that there were files put into the following folders:

Character
Hand
Pose
Props

Now let's say that the files inside the "Character" folder unzipped to something like the following path:   character / JSmith / Daz People / V4 / Hot Dress

Now let's say that the same package unzipped files into the "Pose" folder to something like this:  pose / disco diva /' bling

And that the files in the "Prop" folder came out in the following path:  props / head gear / hat

Now if you were to just  unzip that zip file to the runtime without looking at it first, you would never in a million years be able to relate inside poser what items went with that package you just installed, unless of course it was the only item you had installed in the entire runtime. But that usually isn't the case.

What I do is continuity naming.  I unzip the file into a folder on my desk top, then I look through it and move around files in the folders that I listed above. And I give the new folder that I put them into, the same name throughout each library.  For example let's say the package we installed was called "Disco Diva" and was made by Dr. Geep. I would open the character folder and get rid of that 5 layer tier of folders.  I would instead make one folder and put the files directly into it and I would call that folder  "Dr. Geep - Disco Diva"   and I would do the same for each of the folder of files inside the "Pose" and "Props" and "Hand" folders.  

That way when I went to use "Disco Diva", all I have to do is open up each library folder and if I see "Dr. Geep - Disco Diva" in the library, I know that those files are part of that package that I installed.

"It is good to see ourselves as others see us. Try as we may, we are never
able to know ourselves fully as we are, especially the evil side of us.
This we can do only if we are not angry with our critics but will take in good
heart whatever they might have to say." - Ghandi