AllSync & AllDup

I have a folder with subfolders and thousands of files on one hard disk, and its backup on another drive.
Paths to the base folders are D:\files and E:\files_bkup. The folder structure on both drives is the same.
I select these two folders with subfolders for search
What should I select to display unicate files that exist only in one of these locations (in the original or backup folder incl. subfolders)
and
display files that are different in the same subfolders on D: and E: (have been modified - I use the method byte by byte or MD5).

By now I don't need to display files that have been moved to different folders.
I made some mistakes in multiple files and I need to find only different files in the backup and restore them.

What should I select in the main window?
°Compare files from all source folders
°Compare only files from within the same source folders
°Compare only files between different source folders
?
Are folders D:\files\folder01 and E:\files_bkup\folder01 the same or different folders?
The search results display many files that have not changed, are the same in both locations, because they have not been changed for years.
Selecting "the same folders" displays the same files, that are both on D: and E:
Selecting "different folders" displays files on E: that are different - this is good, but also displays all files on D: that are the same as on E:

Should I temporarily rename the backup folder to E:\files (without _bkup) for better results?
Should I check [ ] Log all files without duplicates? It is checked.
Show only files wihout duplicates is checked.
or should I compare subfolders only (\folder01 on D: and \folder01 on E:) to find only different files or not existing in one of the locations?

Easier to say, I want to copy all files from backup to a new folder. Let's name it D:\files_new
Copy all files from backup there
Find all files in D:\files that are different than D:\files_new
and all files in files_new that are different than D:\files
but only in the same subfolders.

You have to use the option "Compare only files between different source folders".

It doesn't work this way, to compare only files in two various root (base) folders.
Also files in the same root folder are listed, if they have no duplicates in the current folder.
I think it is impossible in AllDup to compare two backups only, no files from the same root folder.

The files in orange frame are the same size, they can be different in content, compared byte by byte they are unique,
but they are in the same root folder - I want to exclude comparing files in the same root folder.
The files in green frame are unique only in this folder (subfolder), but they exist in both root folders and they are the same.

If AllDup finds two the same files in different subfolders, they are not counted as unique.
I think I have to find a different tool. Can AllSync compare two backups, folder by folder and list only different files in the same subfolders of two backups?

Have you activated the search option "Show only files without duplicates at the search result"

Can AllSync compare two backups, folder by folder and list only different files in the same subfolders of two backups?

Yes, AllSync can compare the content of 2 source folders and show different files or missing files.