It seems to depend where they are.
If you have stuff tucked into your windows defined user folders - should be ok .
If you have folders elsewhere - system restore will remove some filetypes.
I have folders on the root of the drive , containing programs I am making/working on, reg files, /dll's etc.
I also put some portable apps. in Program Files, or Program Files (x86).
FYI on this occasion , system restore failed - but still removed a lot of stuff.
I ended up repairing the registry from boot media to fix the original issue.