[support] Disappearing .htaccess File

I've been working on a customer site on my server, and I uploaded it to the client server today. The front page displayed fine, but when I click on any links, I get page not found errors. I'm using clean URLs on my server (like I do on every project), and I noticed that the .htaccess file was missing. I uploaded it twice, but when I go to another folder and come back, it's gone, as if I never uploaded it in the first place. I asked the client about it, and they know of nothing that would do that. Has anybody seen this before, or know how to fix it? Thanks. Steve