At Galaxy Main https://usegalaxy.org, data uploaded using FTP stay in the staging area for three days. This time can vary between Galaxy servers - if working somewhere else, contact the administrators for their staging time window.
No matter where you are working, import the data into a history, using the Upload tool, before that time expires to avoid the need to reload.
- Loading Data >> https://galaxyproject.org/support/loading-data/
Thanks, Jen, Galaxy team