The MS IDE is not required for .NET development. I have used notepad in the past and the compiler is actually part of the runime so you don't need to even go near VS. To be honest I'd be surprised you've only had issues with the saving, VS has a reputation for occasionally hosing a file structure totally.

I have seen people using Eclipse to edit .NET projects so maybe thats worth investigating? it doesn't save the pain for now I know but maybe if you have to do it again.