Visual Studio Custom Controls All stop being known elements?

I have a visual studio project with about 20 custom controls and a dozen or so aspx files to boot.
They are referenced in my web config file.
I added another custom control and soon after every custom control in my code and markup became 'X' is not a known element.
I had seen similar behaviour before in visual studio so closed the program and restarted but to no avail.  I also tried, cleaning and rebuilding.
I tried upgrading the project to a later version of Visual studio (2010 up to 2013) again no avail.
Something I noticed though, if I changed the namespace on the controls to something else the markup references changed from 'is not a known element' to 'is not registered' which suggests that the original references in the web config are being detected in some way.
Has anybody experienced something like this who might be able to offer a suggestion on how to bring the solution back into a 'buildable' state?