I've had to replace 3 64gig cards messing with roms and TWRP recovery unfortunately.
Issues your having sounds very similar to weird problems I've encountered. But night time wasnt the problem lol
Try deleting a file and reboot is the file still there?
Try creating a file and reboot is the file there?
Do it from a PC using cable?
Do it from microsd adapter?
I've even reformatted using PC and phone to find all my files still there and untouched..
Nothing will fix it.. My only solution was copy data and replace on a new card and snap the old card in half for security reasons.
This was after using TWRP and Alliance/Beans roms I've had these issues with a 64gig sdcard. I'd blame it on TWRP somehow.
Sorry it's not a fix.