This is a somewhat common question..
Q: The FTP Server is only showing 10,000 files, but I know the folder contains more.
This is a restriction limit set by many FTP servers in their default configuration to enhance performance and security by truncating the listing. The limit enforced varies between FTP servers, often times the server administrator is unaware of this limit. The ideal solution is to limit the amount of files within a folder, this will make the FTP server run more smoothly.
Many shared hosting providers try to fit as many customers as they can on a single machine and will often times use a limit much lower (During my research I found a provider that enforces a 500 file limit, ouch!)
By removing some files from the folder you'll be able to list the remaining files that were previously truncated from the listing.
If this isn't an option and you have administrative permissions (root access) then you can change the FTP server configuration, this may impact the overall performance of the server. Especially if the server is multifunctional providing additional services such as dns, http, mail, etc. (our advice is to use your best judgement.)
The good news is that this is not a limitation of the FlashFXP software and FlashFXP can display virtually unlimited files (limited to available memory)
Additional Resources
(Copied from http://download.pureftpd.org/pub/pure-ftpd/doc/README)
-L --limitrecursion <number:number>
- '-L <max files>:<max depth>': To avoid stupid denial-of-service attacks (or just CPU hogs), Pure-FTPd never displays more than 10000 files in response to an 'ls' command. Also, a recursive 'ls' (-R) never goes further than 5 subdirectories. You can increase/decrease those limits with the '-L' option.