You didn't mention your operating system. Since different OS versions of Switch support different file types, it's important information. For now, let's assume you use Windows.
If you "right click" on any of the files you are working with in Windows Explorer, what does "properties" tell you about the file? If it says that the file is a ".flac" audio file, then that's what it is, regardless of what the file suffix (the last letters after the dot in the file name) says it is. If anyone simply changed file names, (Example: Heros.flac to Heros.mp3), then that could cause many problems for programs trying to open those files. That would be the first thing to check.
I double-checked the Switch help pages. Their Windows version does support opening ".flac" files. You should have no problem opening and converting those files. Do you remember the exact error message that Switch gives you when you try to convert?
Also, I went to the Winamp home page. Their information doesn't say anything about being able to convert audio files. Winamp can play ".flac" files. It can rip and burn CDs. But as far as I can tell, it can't convert anything other than converting files from a CD to various formats, assuming you have the "Pro" version.