Thanks for the quick and helpful reply, Dennis.
I think I can articulate my ideas about how both of those issues could be handled better, but I'll save that for the suggestions forum.
Another question I have, maybe a little more complicated, has to do with the distinction between a deleted and non-deleted file. I'm guessing from the documentation that a file is defined as "deleted" if Recuva believes that the file was placed in the recycle bin and then emptied (or presumably if the file was "permanently deleted" via Shift-Del or other normal manner), and that it is called "non-deleted" (and ignored by default) otherwise. Is that right or am I oversimplifying things?
But the files I'm trying to recover were not deleted by me, and in fact I don't exactly know how they became lost (or orphaned it would seem - so far it looks like Recuva is recovering them all fine, and not ignoring them). I did a couple of unusual things with the hard drive they were stored on, so pretty clearly that's related, but I'm not sure what caused the problem, and I wonder whether figuring that out can help me to use Recuva more effectively and avoiding problems in the future...
I have a WD 3TB "Red/NASware" SATA drive full of media, mostly video, and I am trying to set up a home media server running on ArchLinux. The drive has one big NTFS partition (4096 block size) holding all the files, and has previously only been attached to a Windows 7 PC. In setting up a server I decided to copy all of the media files onto another 3TB drive that is configured to boot into ArchLinux, with one large ext4 partition to hold the media (it is in fact a hybrid GPT/MBR disk, but I think that's not relevant). I removed the drive (by uninstalling within windows and then physically removing it from the external SATA/USB dock), attached it and the destination drive via internal SATA to my linux box, and started a copy job of about half of my files, letting it run overnight. This morning I saw that the job was finished but there was an error message on 3 or 4 files saying basically "file not found", which seemed odd since all I had done was to type "cp -p /source /destination". The files on the destination drive looked fine, though those few files were missing, and the size of the directory was considerably smaller than expected (maybe 700G instead of 1T). I could tell what some of the missing files were, so I looked at the source drive and sure enough, they were missing there as well. I brought the drive back to Windows and started using Recuva.
My first question related to Recuva (or maybe other recovery software) is whether it might be possible to just recover the files in place, without moving them, in a non- or minimally-destructive way. It seems like all the files' data is still there, they've just become orphaned somehow. I realize there's always some risk that in restoring the directory data for one file you might overwrite some content data for another, but I would be willing to take that risk since they're not mission critical files. If I choose to recover to the same disk in Recuva, will it leave the contents of the lost files in their current locations, with a "best effort" to not overwrite anything else important? Or is there some other method of restoring the directory connections without stepping on anything else?
My second question is perhaps better asked somewhere else, but I'm sort of on a roll I guess. Any idea what is likely to have caused my problem? I have always believed my method of removing the drive from Windows (uninstall through device manager, power down the dock, remove the drive) to be safe, and my ArchLinux box seemed perfectly capable and happy to be dealing with a >2TB drive. What I did with it connected to Linux was minimal - I looked at the disk partitions to make sure Linux was seeing them, and then I ran copy/cp *from* that drive to the other drive.
In poking around I'm seeing some indication that just connecting it to internal SATA might have been a bad idea - something about motherboards seeing it as 512 block size in order to consider it as a boot drive, but I wasn't using it as a boot drive. Anyway, at the moment this seems like th amost promising clue.
If anyone has any helpful knowledge on this, fire it at me...
Thanks again for taking the time to help out (especially if you've actually read all the way to the bottom of this epic)...