Spotlight settings in Settings have changed.

Ian R. Brown wrote:

The only thing I can think of is that I upgraded macOS 15.4 to 15.5 over 3 months ago so does a macOS upgrade reset the preferences (settings)?

A simple way to check is to set the preferences as you want, upgrade to 15.6.1 and see if they change.

Ian R. Brown wrote:

Because Spotlight and mds_stores were writing vast amounts daily on my new M4 mini (and also on my M2 mini) I deselected everything in the Spotlight tab in Settings and also listed all my drives in the Search Privacy section at the bottom to prevent Spotlight from doing anything.

The only thing I can think of is that I upgraded macOS 15.4 to 15.5 over 3 months ago so does a macOS upgrade reset the preferences (settings)?

Bits can get flipped yes, nothing new here— in any update or upgrade. This is why having a current and viable backup is always recommended—in the event things go horribly wrong.

for minor issues like yours, resetting your preferences to suit your needs and carry on.

No one wants to spend time trouble shooting old issues, old bugs if they have already been sorted out with the current updates.

The current stable release of Sequoia including bug fixes, security updates is macOS 15.6.1

Keep your Mac up to date - Apple Support

Keep your Mac up to date - Apple Support

note: "Before installing new software, it's a good idea to back up your Mac."

Update macOS on Mac - Apple Support

I will say issues with mds and spotlight or often resolved by simply rebuilding the Spotlight index manually

Rebuild the Spotlight index on your Mac

Rebuild the Spotlight index on your Mac - Apple Support

you can see it working by entering most anything into the search window

What's new in the updates for macOS Sequoia - Apple Support