I often delete versioned files from Visual Studio without great care for the source control impact. However I eventually have to go through and clean up the mess I made by not properly deleting the files from svn as well as on disk. When you delete a file physically but not in SVN, SVN willl declare the file missing.
For a couple of files a quick "svn delete foo.txt" will take care of the problem. When there are lots of files this is tedious and prone to error. That is, unless you have powershell.
# Used to do a "svn delete" on all missing files
$data = & svn status
foreach ( $entry in $data )
if ( $entry -match "^!\s+(.*)$" )
& svn delete $($matches)