I have no idea how it happened but I had to give today a homework in the university and it wasn't in the pendrive. At the moment I have recovered 1 of 2 files with scalpel (I just love the name of foresnic tools :D).

From the website:

Scalpel is a fast file carver that reads a database of header and footer definitions and extracts matching files from a set of image files or raw device files. Scalpel is filesystem-independent and will carve files from FATx, NTFS, ext2/3, or raw partitions. It is useful for both digital forensics investigation and file recovery. Scalpel resulted from a complete rewrite of foremost 0.69, a popular open source file carver, to enhance performance and decrease memory usage.

Steps

Create an iso image from your pendrive:

sudo dd if=/dev/sdc of=pendrive.iso

Have a look to the example configuration file (required) or copy it to $PWD:

cp /etc/scalpel/scalpel.conf

As I had to recover a C file I added to the end of the config file this line:

echo "c    y       11000     /**" >> scalpel.conf

Which means "find files with 'c' extension, but not 'C' (case sensitive) and read 11000 bytes from the header.
I played with a bit of advantage as I knew for sure the file started with comments as the professor gave us a skeleton file. The length field is not so important but I knew that I had not written 10K of code.

Run scalpel:

scalpel -c scalpel.conf -o recovered pendrive.iso

After that, in the recovered folder I had a log file named "audit.txt" and a folder named "c-0-0". Inside the folder there were a lot of ".c" files, all with length 11000 and that started with "/**" and manually I have found the one that I searched and removed the trailing 11000-true_bytes bytes.

Appart from this manual usage I did, it has preconfigured headers for a lot of filetypes like jpg, avi, doc, pdf, pgp, zip... so that you only need to uncomment the line in scalpel.conf of the files that you are searching.

My pendrive was formatted with FAT32 but it's filesystem-independent.

Kudos to the Scalpel developers!