Let's try to walk through this. These probably aren't the issue but they would be things I would check if troubleshooting:
"I work in a testing center that uses filemaker pro to allow students to sign in, verifies what class they are in and also serves as a record keeper."
Is this file on FileMaker Server? Is it a dedicated server box or do you have it on a network server (using network server would be disaster).
"After this I copy the filemaker pro icon on the desktop and save it on a flash drive. "
If the file is served, is it still open at the time? Served files should be closed before you copy them. Are external backups allowed to run on this directory? Why do you save it to a flash drive? Is it so you have a backup copy or is it then the copy you use going forward?
"In the past few weeks my manager arrives the next day and all of the files from the previous day are erased. "
Can you explain what you mean by erased? Is the file there but all records deleted? Are the records there but all of them blank? Is the file gone? Are only some records missing (the ones you have as a found set the night before)?