Just keep a separate database that tracks the most recent upload per user. Whenever bobby uploads a file, its filename replaces whatever filename was in bobby's database row previously. And whenever someone accesses bobby's page, the database is checked to see which file was most recently uploaded by bobby.

It's not a good solution to sort a list only to obtain the single newest. It's a better solution to either keep track of which one is newest, or do a linear search for the newest. In this particular case, I think you're just better off keeping track from the outset so you never have to search through 500,000 files.

For simple database solutions, you could have a look at DBD::SQLite, and of course, DBI. Or perhaps your web server provider already has some other database installed that they'll let you use too.