I had this same problem. I reset my phone one day and lost the Skype beta app I had. Fortunately when I logged into the Market it was in my list of downloads and let me download and install it again. I was fortunate to get it back but I never did see it in the market after that.
I thought to myself I better back this application up or I might lose it for good. I found another free app called ES file manager and backed up the one I had right away. I am posting a copy of it here on my blog for anyone that may need it.