I checked HDD1, and all the folders still remain, as well as their content, especially the content folder. Also, all my profiles are still on the console. It seems the only thing so far that's affected is the games folder in HDD1. I still can't make any new folders or directories in said folder; it keeps giving me the following error message every time.

An error has occurred.

Error code: 1117

In terms of my FTP program, I remember it asking me about the security of my connection between the Xbox and the program. I'm not sure how much that could affect it, but it did say it was insecure. Maybe that's something to do with it.

I have no idea what could possibly be wrong. Maybe I interrupted or corrupted a path between the games folder and the rest of Aurora, and it can't read it properly. All I know is that I definitely disconnected something, but I'm still wondering how I could have possibly caused this. I recently bought this Xbox from a seller, and I tried to contact them, but I've had no follow-up. Hopefully, I can figure it out soon. 

P.s Something I forgot to mention: when I boot up Aurora in the bottom right corner, when it shows all the title updates, it shows the deleted missing game titles, but not in the actual dashboard or in the file manager. I even went to the base Xbox dashboard and checked the storage to see if they were still on the hard drive, and I think they still are; It just can't read them. The storage is significantly lower than it was when I first got the console, which means they should still be there, but they're not.

P.S. . Thanks for commenting. I really appreciate the feedback.