I have a Visual Studio 2013 solution that is under source control (TFS, Visual Studio Online). It is mapped to a local workspace, I have checked out some files (e.g. web.config,
I had the same problem with only one html file in a project. For me it seems to have something to do with VPN that I was using to upload this html file to CRM system. Whenever it was on it seemed to "block" the file somehow. When I closed the window where I was uploading the html file I can save without any issues.
It turns out this was caused by disk encryption software. Disabling the disk encryption software services each time after starting VS2013 solves the problem. I did not have this problem with earlier versions of Visual Studio, presumably because of the new copy-replace cycle adopted by VS2013 mentioned in EDIT 2 in my original question.
Apologies for not coming back to comment and answer my original question, I completely forgot about it.
martijn_himself sounds correct, problem could be because of Disk Encryption Software. This problem started om my PC when i changed settings (domain etc) on Disk Encryption Software. and a simple "Update 2" for VS2013 fixed this issue.
For me, it was Windows' Controlled Folder Access, even though I didn't get the standard warning/error. In "Allow an app through...", I had to add
C:\Program Files (x86)\Microsoft Visual Studio 12.0\Common7\IDE\WDExpress.exe
For me it was Google Drive. Once I've closed it, I was able to save the file.
Try running Visual Studio as Administrator.