it's truly sad that you had to lose files to expose this flaw, I hope you can recover them. I never use OIV unless it is on an absolutely clean game, simply because I don't trust the package system and I don't trust the people who build the OIV packages. I usually manual install it, so I have never checked the assembly.xml.
ENB and Reshade are optional installs for QuantV, so it shouldn't do anything with ENB or Reshade related files, unless you specifically use that optional installer. Whilst it does say in the readme "Install on clean game only", there's no mention that existing files in the game folder will be deleted and that's really bad. but in this instance I can't defend them. I'd love to be able defend the mod author, because QuantV is the only graphics mod I ever use. unless OpenIV just outright deletes things completely. You should be able to recover the files from the recycle bin though, if you haven't already emptied it.
There's certainly no excuse for file-deletion without warning, ever. nothing should ever be allowed to delete something it didn't create (in an installation/uninstallation sense anyway). OpenIV team, I know it's a bit long to read but please bear with me and consider doing this.