I found a solution to this problem.
In general, as it turned out, it was necessary to delete not only manifests and all directories associated with the deleted system file/folder in winsxs folder,
and also all related directories in the registry along the path: "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\SideBySide\Winners".
If done correctly, sfc /scannow will eventually ignore a specific system file/folder path.
I also forgot to add that in some cases cleaning is also required along the path in the registry: "HKEY_LOCAL_MACHINE\COMPONENTS\DerivedData\Components"
In addition, clearing winsxs paths and manifests associated with a system file/folder is not necessary, since by editing the registry, sfc /scannow will ignore them.
However, you can also clean up winsxs to save space.