Restarting MacOS sometimes causes desktops to be confused

Desktops are not document-centric. They are assigned to Applications like Finder. It has no capability to assign particular document windows to a particular Desktop. There doesn't seem to be a way for an App to control that type of functionality.

MBonnice wrote:

I have nine desktops, each of which have different Finder folders open, located at specific spots on the desktop.

Occasionally, when the computer is restarted, the first desktop is not the one that is opened but a different one is. Sometimes the windows in one desktop appear in a different one instead. Sometimes windows disappear entirely.

I'm using Catalina 10.15.3, on MacBook Pro, but I remember this happening in the previous version of the OS.

What bugs me is having to manually rebuild all the desktops.

What I want is to know which preferences file contains the desktops setups. I'll make a copy of that file then if the computer starts up incorrectly I'll restore it and restart.

You do not say what exact Mac /model /year /size /retina /touchbar is this

or

w̶h̶a̶t̶ ̶e̶x̶a̶c̶t̶ ̶m̶a̶c̶O̶S̶ ̶y̶o̶u̶ ̶a̶r̶e̶ ̶c̶u̶r̶r̶e̶n̶t̶l̶y̶ ̶r̶u̶n̶n̶i̶n̶g̶?̶ ̶<Catalina 10.15.3, on MacBook Pro,>

Verify your software is up to date.

How much RAM does your machine have?

How much free storage space would be another consideration(?) for scratch & swap files.

You can look at Activity Monitor.app at "memory pressure" for some insight if you are overloading the machine RAM to caused by this juggling of Desktops to cause the confusion.

How to use Activity Monitor on your Mac - Apple Support

Possibly 10.15.4 and up may lend itself to stability issue you "occasionally " see.

Not sure if there is a software fix here— you can file your user experience with the macOS user interface

Apple Feedback http://www.apple.com/feedback

Nine Desktops /open finder windows— I am not sure what the record is but this seems like a lot to me.

Maybe as an experiment cut that number in half and test for a while(?) There is a limit, don't you suspect?

I can add— with 16GB of RAM I always have at least 15-18 apps running all the time : from the HUD (heads up display) Command Tab

and of those 8 of those in Full Screen— and no issues. From Mission Control

https://support.apple.com/guide/mac-help/work-in-multiple-spaces-mh14112/mac

Rarely do I open a new Desktop however— to isolated a particular activity.

A basic fix is to boot into Safe Mode (Use Safe Mode to isolate issues with your Mac and Playing Safe: what does Safe Mode Do?).  Reboot normally and test again.

NOTE: Safe Mode boot can take up to 10 minutes as it's doing some system cache cleaning, volume verifying and directory repairing. 

Can't help you there as I don't use multiple desktops so have no idea which preference file would control them. Safe mode shouldn't delete any preference file it only removes temp cache, system and swap files.

I'm talking about the behavior of Finder, not of any other application.

It doesn't matter which application you are talking about. They all work the same.

You might try the Saved Application State. Each app has a folder in ~/Library/Saved Application State/