Help: files pushed with adb are now almost completely invisible

I have been using Nitrogen OS on my OnePlus 3T. I decided to try a Pie ROM, didn't like it, and wanted to revert back. I was having issues with TWRP mounting storage, so I decided to back everything up and wipe.

I used adb to pull the entire sdcard to my computer and verified all the files. I did a complete wipe in TWRP, then pushed the entire sdcard directory back to the phone. I verified everything was there with TWRP, then used it to restore from my last backup, and rebooted. Everything was totally normal.

Now, a day later, I've noticed that my files are not appearing in file managers. I don't know when this happened, whether it was first restart or what. They are on the phone, and taking up space, as can be verified with DiskUsage app, but they are just listed as 40 GB of "System data." See attached screenshot. My Files app can actually show some files, but they are listed as "Unsuccessful" and have no other info. See other attached screenshot. They no longer list in TWRP file manager either.

What gives? How did my files get turned invisible and "unsuccessful"? And can I get them back into usable files? Should I wipe, push backup file, restore, then push the rest?
Side note: TWRP now constantly asks about system modification, despite ticking the box to never ask again every time.

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