You can remove all project items but you should only edit/alter code items that are NOT contained in folders that begin with an underscore such as _core and _library. Each project physically only contains your source files. Folders with a leading underscore contain links to shared source code created by other people such as arduino core files and libraries.

Warning: If you alter the code in linked source files such as, core or library, then it will alter (or break) all of your arduino projects

Q: What if I remove a linked file by mistake?

You can add the files back into the project manually or use the menus to re-add the items. For example if you have unlinked a vital _core file then use the tool bar to reselect the board, if you have removed a _library item then remove the entire library folder from visual studio and re-add the library using the tool bar.

Q: What happens when i select delete on project items in the solution explorer?

Linked items are unlinked but are not deleted.

If you attempt to delete a source file then Visual Studio will show you a warning. If you click OK then your source file will be permanently deleted!