It seems that there is malicious content present in your data and the security system removed the files. Please restore the data and then scan the whole data, when it will be cleaned then you will be not face the issue again.


any one can tell me how to know which data is harmful for cpanel
and is it legal to delete my files when alot of people uploading data on my website

My hosting has virus checker that will tell which one are problematic.
You should ask hosting at least what folder it is, download it, run anti-virus on that folder.
From my experience hosting virus checkers are often false positive, ie it mark all modules of this forum script as malware