This is the same to this question: Can't delete file in download folder
But for me the answer is not clear, as per the OP's answer 'he turned on the SD Maid app' but did not stated what option in SD Maid resolved the issue. The OP stated as well 'he deleted the whole directory' but not specified if using SD Maid or PC.
We have the same scenario where I redownloaded the same file and after copying it to the exact location where I'm having issue it made two identical files and what I tried so far:
- Highlighted both items and deleted it using SD Maid, it says success but after refresh it retain the other file with 0 byte.
- Connected my phone to PC as MTP and tried to delete it from there and what I noticed it only shows one file unlike looking in the any Android file manager. It says success but checking it again in the phone it retain still the file with 0 byte.
- Tried apps in playstore that says secure delete that uses different algorithm but still after it says yes the same scenario occur above.
- Perform wipe cache partition in the stock recovery
- Clear data and cache of stock file manager
I know my last resort would be complete factory reset, but is there any other way?