FTP says, 'Truncated To 2000 Matches'

My entire website is in FTP like it should but all the sudden, a couple of times it has said, after it is connected, that 'The output truncated to 2000 matches.' FTP will NOT show more than 2000 matches in the public_html folder/list and the disk space used is not accurate.
Also, when I connect to FTP, the public_hmtl folder is gone because it says this. And my entire website was gone (aka deleted) and the web hosting company and myself had to reupload my entire site and it did that when it stated, 'truncated to 2000 matches'. After we got my site back up, FTP worked fine until now, it says this again and my public_html folder is gone. I have to type it in manually to get it to come up. Now I'm just afraid that my site will be deleted again and I DO NOT want this to happen again! Please help!


Make directories to skip that limit, having 2000 files on a single directory is a bad idea.