Will changing script editors affect my code?

I use both Notepad++ for javascript and Visual Studio for C#. If I was to write a script for something in C# with Visual Studio and then I wanted to write something else in javascript and switched over to Notepad++ as my editor (in preferences under external script editor) would it mess up my previous C# code? My fear is that one of my editors does not support the other language and when I switch I will have scripts that no longer work?

No that is perfectly safe. Visual Studio might sometimes complain about line endings, but it is harmless. An editor will not change or mess up already created scripts just because it does not have support for that specific language.