Photoshop saves disappearing

Using Photoshop CC; on Windows 11

I have just switched from using Photoshop CS5 and Bridge, which I have been using since university more than a decade ago to now using Photoshop CC and Lightroom. I am working on compiling a photo book for a client and I shoot in raw. For my typical workflow, for every project I have a RAW folder with all photos, which I rate and then open the raws to edit. After edits, I save the edited file renamed into a Processed folder, so as to keep the RAW file in it's original state. After all processing has been done, I typically batch process the images into JPGS and have them save in a JPG folder for the project. 

Problem: Trying to follow this workflow in the new Photoshop CC ecosystem seems to not work at all. I just spent all night editing 50 photos and saving them to a Processed folder, and while photoshop is open, I can see them there in Windows Explorer, but once I closed photoshop at the end of the night, all of my photos except for one dissapeared from Explorer in the Processed folder. What is happening here? Why are my photos disappearing after being saved?