Are you sure it’s 998 files? Not 9998?
When trying to list the Album-Art folder in FileZilla with logging enabled, I see the server saying this:
Response: 226-Options: -a -l
Response: 226 Output truncated to 10000 matches
Status: Directory listing of "/htdocs/Album-Art" successful
9998 files, plus . (current directory) and .. (upper directory) makes 1000 entries in the listing. So that all makes sense.
So it seems that our FTP server won’t list more than 10k files. And given how long it took for that listing to be generated, I think it makes sense to have a limit on the number of files, and than 10k is a reasonable limit.
FileZilla also struggles with the number of files, scrolling through them is quite choppy.
This appears to be a setting that can only be changed for the entire FTP server, not for individual accounts.
So I’m afraid that this is simply expected behavior. And it’s up to you to figure out how to best deal with it. If reorganizing the files is not an option, maybe you’ll just have to accept that you may need to upload images without being able to verify that their upload was successful.