After the new update Vortex replaced incorrect files of a one mod with files from another mod within Vortex mod folders. this is pretty hard to explain and English is not my first.
When Mod X loads after Mod Y (conflicting files), Vortex will actually try replace the files of the Mod Y with the files of Mod X within the vortex mod folder of the Y. The result is that you have identical files in the both mod folders X and Y.
Normally Vortex doesn't touch the files, just changes which files are deployed to the game folder.
So when I had the Mod X being deployed, Vortex asks if i want to deploy the changes in the Mod Y, but there were no changes being made, just Mod X that loads after Mod Y. In a hurry I didn't realize this and clicked deploy. The files that were in a totally different vortex mod folders were now replaced with the files from a totally different mod folder. And this actually happened to all of the mod folders the Mod X had conflict with. In other words: Vortex replaced/destroyed the Mod Y files in the vortex mod folder. Vortex should have not made changes into those files.
I just lost a punch of mods/files made by me due to this bc I didn't realize what Vortex was doing before it was too late.
Also if you think of commenting to this topic "Yeah right you just dum" (like someone already did) or in the lines of like I made this up for laughs bc I totally have no better things to do like consider: a. maybe you are not a software dev b. maybe your need of attention is not my problem. I have 600+ mods in use, made a few, I'm not making stuff up. I'm just letting people who actually develop the program know and warning others to watch out for this.