To try to answer your questions
Yes- if you delete fonts from your font folder you will get a font missing- font substitution message when you try to re-open a LO that used the deleted font (PSP and PSE experience-don't know about other programs.
You can copy the fonts to another folder without any problem...just have a different name and location---but most programs will only "read" from the windows font folder (I think).
I have several different folders with fonts (in the organizing process myself). I use The Font Thing to browse the folders for what I want. You have the option to "load" or "install" the font.
This way I can keep the Windows Font Folder a bit more tidy so the font dropdown list isn't so long in my program.
I'm really tired hope this makes sense.LOL