Is there a way to make DOpus 12 handle archive files without having it use the preview icons that come with DOpus? I know that disabling Display Thumbnails for Folders works but I want folders to show files within them on the thumbnails instead of having them use the empty icons.
Click the link next to that option to open the dialog shown below, and set the first two checkboxes as shown:
You'll then get the same folder thumbnails as you should see in File Explorer, with archives not showing any contents, and folders showing contents.
One difference is it will be the shell's style of 3D folders rather than Opus's style of flat folders.
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Can you set it so that DOpus doesn't use flat icons for anything even if it handles the file types that use them?
The settings in my screenshot will do that (assuming you have non-flat icons for the archive file types; it'll use whatever icons they are set to use).
Well that disables the folder contents from being shown within the folders in thumbnails mode so it only shows empty folder icons. What I want is DOpus to handle Archive files but to not have to have the folders show as empty in thumbnails mode, and I don't want it to use these for zips.
How it looks, (with internal handing on):
What I want it to look like, (With internal handling on):
With those settings, you'll 3D thumbnails, with contents for folders, and without contents for archives. It should look the same as in File Explorer.
If that's not what you want, I'm confused at this point. 
If I use DOpus to open zip archives it automatically changes the thumbnails to the ones in the first screenshot in my third post, if I disable the options that you told me to it shows all folders as using the empty icon, I would like DOpus to leave the ZIP icons as the ones shown in my second screenshot without having to disable Generate folder thumbnails from images within folders.
Are you turning on/off the options so they look like in my screenshot above?
That should give you what you want, if I've understood correctly.
Unless I'm misuderstanding, he wants the same thing I asked about a few days ago... to be able to see the thumbnail of the first image in the archive.