I often zip up my backups, or make the files read-only, to avoid doing that by accident. (Read-only either by the read-only attribute or, for something stronger, by using NTFS file permissions. The latter will also protect you, to some degree, from viruses which might try to erase your backups, although a clever virus could change the permissions back and delete the files.)
Have you tried using the Synchronize tool in Opus? It has a two-way copy mode which will copy the newer versions of the files from each directory to the other so that both end up the same. You could also do a one-way copy using the date as the criteria, where it would copy from one directory to the other, overwriting any files in the destination which are older than those in the source.
This is no good if you've made changes to the same files in both directories, since both versions are effectively new and wanted. You'll have to merge the changes together can't simply overwrite one file with the other. But if you haven't done that then the synchronize tool might be the best solution.
Another option is to use the Copy Update-All or Copy Update-Existing functions. The first of these can be told to copy/skip/rename things based on attributes like file dates. The exact command you will need depends on exactly what you want to do, but have a look in the PDF manual at the arguments you can give the Copy command for an idea of what it can do. Let us know if you get stuck there. The Synchronize tool is a much easier thing to use, if it's suitable (i.e. you haven't made changes to the same file in two places).
Only certain operations can be undone. If you overwrite a file then the old file is gone and doesn't exist anywhere to be copied back.
You can set the duplicate finder to consider files as duplicates if they have the same filename and size or the same MD5 checksum (i.e. the same file contents). The delete mode simply deletes all but one of the duplicates. You can get some control over which duplicate is kept by sorting the file list and then scanning a second time. The first file is always kept, so if you sort by date (newest first) then the newest file will be kept and the older ones deleted.
Opus is probably set to delete to the recycle bin, in which case it uses the same (lame) function that Explorer does since there isn't any other interface to the recycle bin in Windows.
If you turn off the recycle bin in Opus, or use a toolbar button which specifies that it shouldn't be used, then you will get better error handling. (But you also won't have an undo since the files are really deleted and no longer exist anywhere to be restored.)
By default you can hold Shift and click the delete button on the toolbar to delete without using the recycle bin. The toolbar delete button should have the same effect as the Delete button in the Duplicate finder.