NTFS → only testdisk available, beside it supports more file systems (also EXT2/3/4).
EXT3 → ext3grep
EXT4 → ext4magic
What kind of files/folders are these?
What program access it?
What have you done?
Maybe you unplug the USB HDD while it was syncing the files to the disk in the background?
Anyway… it is bad idea to use a NTFS Partition for backups in Linux, likewise Ext4 in Windows. For exchange between systems, why not, but not for backups.