Re-download to another directory and compare to your home directory.
Checking 60 objects can be done by hand. E.g. if foo is in the other directory then most likely foo in your home directory is from the download. If bar is in your home directory but not in the other directory then most likely it's not related to the download.
It may be some subdirectory was ...
As discussed in the comments, this was most likely due to new hard disk being mounted while dd was being performed. After dd completed, new hard disk was unmounted. This might have caused superblock on the new hdd to be overwritten.
You can make a copy of it, but opening it directly "in place" doesn't work.
That is usually caused by the file being locked by someone else on the network.
That doesn't mean that is actively in-use by someone. It is possible that someone had it open previously (could even have been yourself) and it wasn't properly closed. That sometimes happens if ...
Those files had gone before du had the chance to explore them. They existed when du explored the directory in which they existed. No general index, each directory is in fact a separate file. I think you can ignore those errors. Eg. "2>/dev/null".
The most common cause for such a problem is that the source file is a
a sparse file is a type of computer file that attempts to use file system space more efficiently when the file itself is partially empty. This is achieved by writing brief information (metadata) representing the empty blocks to disk instead of the actual "empty" ...