How data gets hidden?
I rebooted by system and checked these flash drive in linux what I found that there was a folder with no name and after double clicking it all my data in those flash drive was visible to me I copied all the data from both the flash drives and kept on my local hard drive, reformatted the flash drives and put them back and then I was able to see all my data normally as earlier.
Only thing which hits my mind after removal of malware why the data was not visible and how could have the malware done so. Does this also happens to the data on local drive too or only on flash drive? and how data was visible in linux?