Hello Fatema,
Regarding the "5235a458..." file ("SM-1.pdf"), you say that "it seems an empty file". The problem here is that "seems" is a bit ambiguous. What is the actual file size? According to the six database records, it is a 204201 byte PDF file. So here we have a consistent value. The records also show that the file was uploaded several times (by the Moodle admin) but there is only one actual instance being used within Moodle (as a resource). Please check again to determine the actual size of the file. If it is a non-zero file, then copy it to another directory (outside of your web-related directories) and try to open it.
Permissions look fine, though you could set it to 0770:
http://docs.moodle.org/20/en/Creating_Moodle_site_data_directory
http://docs.moodle.org/22/en/Security_recommendations
I see you have full access to the server. What OS are you working with?
Did you check about any non-standard Moodle plugins?
You didn't mention anything about the following advice:
- If everything happened after the server issue, did you start by checking that the server is actually without any problems anymore? Check your server (web and database) configuration files and error logs (very important).
- Please enable debugging: http://docs.moodle.org/26/en/Debugging
These two recommendations are fundamental in trying to determine the cause of the problem.
Regarding the server settings:
- Apache - Check the LimitRequestBody directive.
- PHP - Check the following:
- file_uploads
- post_max_size
- upload_max_filesize
- memory_limit
- max_input_time
- max_execution_time
Also check for any .htaccess (dot htaccess) file that could be interfering.