I am using Photos input to bring in a folder. When changing the order of photos in the SlideShow settings, the order will change after vMix is closed and reopened.

So if the folder contains A.png, B.png, C.png

Change order to
C, B, A

After save and restart the order will be something like
C, A, B

Is there a way to make the change persistent between sessions?

just rename your images in the folder so that they show in the right order. It's way quicker and simpler to do than anything else or re-doing over and over the same changes.

I always do this
01.jpg
02.jpg
03.jpg

as easy as A B C

There is a difference between list (photos from a folder) and playlist (by adding inputs)!
The way folders are sorted is not under vMix's control

there are probably more is one googles
https://superuser.com/qu...lly-according-to-the-sor

Not sure but the fact that the list is taking from the content of a folder which can change when vMix is not open compared to the inputs vMix knows the details of ( location etc) makes vMix treat it differently in terms of keeping track of in its settings
When opening an setup and vMix doesn't find an input one gets an error (or question to change) for a folder it's the folder location and name that's important but having to check all it's content seems to be a bit impractical in my view . For a playlist its just keeping track of the references to an existing input (list of numbers)
Changing orders once open isnt a big deal , keeping track of it all for future is a different story . anyway to me it makes sense (programatically)

but as pointed out , the easiest solution is to name the files in order just like the image sequence for stingers etc