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I have a 2TB external HDD (/dev/sda), formatted as NTFS. Recently, it started giving me "Input/output error" when moving files and strange output to the ls command, like

...
??????????? folder_1
?   ?   ?   folder_2
ls: cannot access 'folder_3': Input/output error
ls: cannot open directory 'folder_3': Input/output error
...

I had a new 4TB HDD (/dev/sdb), so I tried using ddrescue to copy the files before a disk-failure, with the command

ddrescue -f -r3 /dev/sda /dev/sdb mapfile

as reported here and here.

The command completed in about 6 hours and reported no error but the "Input/Output error" are still present in the new drive, i.e. when I try to run ls on the new drive it still gives me the same output as before.

I tried opening the new drive from Windows, which warns me about something "to fix" on the external drive (although it did the same with the old drive) and I tried giving him a chance. After "fixing" the new drive in Windows, there are no more "Input/output error" messages but the folders are gone, namely there are no folder_1, folder_2 and folder_3 on the new drive.

Here is the output of smartctl -a /dev/sda

ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE
  1 Raw_Read_Error_Rate     0x000b   100   100   050    Pre-fail  Always       -       0
  2 Throughput_Performance  0x0005   100   100   050    Pre-fail  Offline      -       0
  3 Spin_Up_Time            0x0027   100   100   001    Pre-fail  Always       -       2107
  4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       320
  5 Reallocated_Sector_Ct   0x0033   100   100   050    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x000b   100   100   050    Pre-fail  Always       -       0
  8 Seek_Time_Performance   0x0005   100   100   050    Pre-fail  Offline      -       0
  9 Power_On_Hours          0x0032   100   100   000    Old_age   Always       -       103
 10 Spin_Retry_Count        0x0033   106   100   030    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       189
191 G-Sense_Error_Rate      0x0032   100   100   000    Old_age   Always       -       19
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       105
193 Load_Cycle_Count        0x0032   100   100   000    Old_age   Always       -       1166
194 Temperature_Celsius     0x0022   100   100   000    Old_age   Always       -       15 (Min/Max 13/46)
196 Reallocated_Event_Count 0x0032   100   100   000    Old_age   Always       -       0
197 Current_Pending_Sector  0x0032   100   100   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0030   100   100   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x0032   200   253   000    Old_age   Always       -       0
220 Disk_Shift              0x0002   100   100   000    Old_age   Always       -       0
222 Loaded_Hours            0x0032   100   100   000    Old_age   Always       -       53
223 Load_Retry_Count        0x0032   100   100   000    Old_age   Always       -       0
224 Load_Friction           0x0022   100   100   000    Old_age   Always       -       0
226 Load-in_Time            0x0026   100   100   000    Old_age   Always       -       181
240 Head_Flying_Hours       0x0001   100   100   001    Pre-fail  Offline      -       0

which, according to this table, looks "fine" (I guess).

So, my questions are:

  1. is there a way to recover "all" the data from the old drive?
  2. in case the answer to 1. is "No." which is the "next step" I should take? Because using ddrescue only to find the same errors on the new drive doesn't seem like a solution.
  3. should I format the new drive with a particular filesystem (e.g. exFAT) and just copy all the files (e.g. with rsync) from the old drive into the new one?
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From the hints you collected, it looks like the problem is not at the disk physical level, but at the filesystem structure level. Some data structures (probably directories) have been corrupted. I can guess that the I/O errors come from stray pointers in the directory structure, which instruct the kernel filesystem to access the disk at impossible locations, or something like that.

I would have done the same as you did (ddrescue to a separate disk) for a start. I'd keep one of the two copies as a read-only backup while you experiment with recovering from the other one.

Then I would copy the accessible files to a new partition (be it ntfs or whatever, does not matter).

Then I would try to recover the rest by means of some low-level tools. I don't know of any tools specific to ntfs, but I'd bet they exist. If the data is of high value, you could try a professional service: they will be most certainly able to recover whatever can be recovered.

If you want to try yourself, recoverjpeg and recovermov are able to rescue your .jpeg and .mov files even if the directory containing those files was corrupted, assuming the data files are not corrupted themselves and they are contiguous on disk.

Black magic is needed to recover other data files. It involves finding some ntfs-specific tool, or a big-file binary editor to search for file signatures (those used by the file command) and browse through the data to recognise them and find the beginning and end of files (assuming they are contiguous on disk).

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