There are 2 kinds of remove:
The Basic Delete (the recycle icon in Library view): Applies to selected books and needs a confirm.
This removes Everything About the book as well.
Then there is what we call 'The Empty Book'.
This leaves the entry in the list, but has no actual book files (except cover.jpg and metadata.opf, which are fairly small)
To create this from a former entry (with a format)
Select Books: Right-click:Remove:All Formats (confirm)

Since you have a DVD backup, why not apply a tag 'On DVD ###'