The TOC does not care what the file names are, just that the entry points to one that exists.
Sensible names are for Humans (most who normally do not see those)
The order of files (echoed in the NCX) governs the reading order. I frequently move files I consider 'fluff', but want to keep, to the end. I never touche the TOC (FWIW If you delete a file, in the EDITOR, it removes the TOC entry, no need to fix that
)