iTunes Library with Roon

I have around 765 albums in iTunes on an external HDD and I have been backing up these using SuperDuper. I have also switched the HDD
I’ve used for my library in playback on a couple of computers. Anyway, I
have noticed a small number of albums don’t appear on my “Main Music”
folder but are in my “iTunes Media” folder.

This doesn’t make any difference when I play music through iTunes but
some albums didn’t appear in Roon, thought a bit of fiddling around and
selecting both folders for Roon to use solved this.

I’ve always found iTunes file management to be confusing and I’m not
sure how this has come about but I’m wondering if I should use the
option to consolidate all my files in iTunes. I believe this would copy
everything into the iTunes Media folder thus giving me a massive
library. Should I

a) Do this and then once everything is in “iTunes Media” folder just delete everything from the “Main Music” folder?

b) Drag my files from the iTunes media folder into the Main Music folder

c) Do nothing

Seems odd that this has happened and I’m not sure why. I have the option
to copy everything to the iTunes Media folder when adding to Library
ticked but clearly that hasn’t happened and folders have been sent to
either one or the other of these folders.