Up to date Windows 10/calibre 6.5 here.
I have had my calibre libraries on internal and USB HDDs for over a decade, and I have had no similar problems.
The metadata elements I care most about are Title and Authors. And, because I edit metadata in the book list rather than the metadata edit dialogue, after editing either cell, the folder and file shuffle happens as soon as I tab out of the cell. If I change both columns, the folder/file shuffle is done twice, this often happens especially when I add articles to my Journals library .
What happens if you move a folder containing a few files with Windows File Explorer that is NOT within a calibre library? Like so:
As far as I know Calibre and Windows/NTFS move files and folder in the same way - via hardlink construction and destruction - i.e. the file content isn't copied, the MFT (Master File Table) is updated. And both happen more or less instantly.
My newish Dell XPS has a PCie M.2 SSD (256GB). So, for curiosities sake I tried putting my Books library on it. Made no observable difference to calibre performance - which was already PDQ on my Windows and X1 Indexed, Compressed, AV visible, HDD drive - so I put it back on the HDD.
- maybe your power management settings are spinning the internal hard disk drive down too damn fast.
BR