I have a problem where I delete an older version of a page layout but it keeps coming back and the changes I made to that page layout do not take effect. I would like to know if there is a way to make SharePoint 2010 always overwrite all files when doing a deployment to a server.
Typically that kind of problem is caused by a customized page layout. With customized I mean that the page layout was modified after deployment (e.g. with SharePoint designer) and is stored in the content database. If so, you have to uncustomize the page before it can be updated via a WSP solution. You can use the re-ghost tool for that: http://stsadm.blogspot.com/2007/09/re-ghosting-pages.html
Files can also be customized by SharePoint (without a user modifying it) if the mark-up code (ASPX page) has errors.