Files upload through FTP remain in the transfer area for about 3 days on the public Main Galaxy server at http://usegalaxy.org. Data should be transferred into a history with the "Upload" tool within that time frame.
Other Galaxy servers can have a different time frame when FTP is enabled. If you are not working on Main, then contacting the group that supports that other server is the best way to learn about their FTP data retention policy.
More about the FTP process:
Thanks, Jen, Galaxy team