Just tested with Focal's Nautilus 1:3.36.3-0ubuntu1.20.04.1 and this
does not happen.

Followed the same scenario and renamed 2 out of 4 sample files:

1) Using Nautilus itself.
2) Closed Nautilus and renamed the files in terminal. 

In both cases Nautilus automatically regenerated the thumbnails.

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https://bugs.launchpad.net/bugs/1879169

Title:
  Thumbs never updated after renaming a bunch of image files

Status in nautilus package in Ubuntu:
  Confirmed

Bug description:
  I refuse to waste my time reporting this upstream, since Gnome
  developers (or at least Nautilus developers) have proven in several
  occasions to be a bunch of idiots unable to deal with bug reports (or
  with bugs in general). You deal with them.

  I had a folder containing a bunch of image files, namely .png files,
  named 1.png, 2.png .... up to 100.png and more.

  I deleted many of them and then renamed the remaining ones to 1.png
  through 21.png.

  Now I look at the folder and all the thumbs have not been updated. For
  example, the thumb of say 5.png is the thumb of the image that used to
  be called 5.png before renaming.

  Even hitting f5 does not rebuild the thumbs, and if I right-click on
  the folder I don't see any option in the context menu to manually
  force-rebuild the thumns (which shouldn't be necessary in the first
  place but should be something I'd be able to do).

  It's obvious that renaming files should invalidate the thumbs cache.
  Fucking pathetic.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: nautilus 1:3.18.4.is.3.14.3-0ubuntu6
  ProcVersionSignature: Ubuntu 4.4.0-173.203-generic 4.4.208
  Uname: Linux 4.4.0-173-generic x86_64
  NonfreeKernelModules: nvidia_uvm nvidia
  ApportVersion: 2.20.1-0ubuntu2.23
  Architecture: amd64
  CurrentDesktop: Unity
  Date: Sun May 17 17:36:04 2020
  GsettingsChanges:
   b'org.gnome.nautilus.window-state' b'sidebar-width' b'192'
   b'org.gnome.nautilus.window-state' b'geometry' b"'1321x879+1501+562'"
   b'org.gnome.nautilus.list-view' b'use-tree-view' b'true'
   b'org.gnome.nautilus.list-view' b'default-column-order' b"['name', 'size', 
'type', 'date_modified', 'date_accessed', 'owner', 'group', 'permissions', 
'mime_type', 'where']"
  InstallationDate: Installed on 2013-10-11 (2409 days ago)
  InstallationMedia: Ubuntu 13.04 "Raring Ringtail" - Release amd64 (20130424)
  SourcePackage: nautilus
  UpgradeStatus: No upgrade log present (probably fresh install)

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