Hi,
I faced a similar situation some time ago. In my case the reason for the unintended desktop icons chaos was not a "glitch", as such (ie a bug), but the result of a caja "feature": I had accidentally triggered the caja right-click menu option "Organize desktop by name", from which there is no escape or undo.
This prompted me to write a set of short python scripts which can "automatically" save and (if necessary) later restore the desktop state by moving the icons to their previously saved positions.
I have now succesfully tested it on several occasions by first moving icons around to random positions and then running the "restorer" script, so I feel confident that, at least for me, it will work as intended, saving the day should the desktop order happen to become totally jumbled once more.
I posted about this here: Disable "organize desktop by name" option.
The scripts are here: https://github.com/moof-moof/Icon-pycon.
The code is basically a stripped down, GUI-less version of a QT-based python scripts by RockDoctor: https://www.linuxquestions.org/questions/linux-desktop-74/where-does-mate-store-the-positions-of-desktop-icons-4175671530/#post6208138 (as I see Norbert_x already mentioned).