User permissions broken after admin account disappeared.

I came home the other day and woke my Mac up from a sleep. I have it set to require my password immediately at wake up.

Going through the usual process of logging in, I typed in my password, only to be refused entry.

"How strange, I must've misspelt it."

I tried multiple times, scratching my head as to why this was happening - I was definitely inputting it correctly. I realised shortly after that I was trying to log in to the "other" account, and that my admin account wasn't displaying as an option.

To work around this, I needed to boot in recovery mode, type a command that removed a file to trick the Mac into thinking it hadn't been set up before, and create a brand new admin account.

(I did this with the help of a YouTube tutorial)

Using this account, I was able to browse my hard drive to see if the account had been totally wiped or just wasn't showing. Turns out, the account was in fact still there, however it wasn't showing when I tried to log in, nor was it showing in "Users and Groups" under settings. Why?

I then updated the OS to High Sierra, thinking this would reset/refresh everything and fix the issue. It didn't. And now the system is noticeably slower, yay.

I then needed to create yet another account under the same name as the account that had disappeared. This linked the account up with all the data, and allowed me to log in, finally.

The problem now though, is that some apps seems to have issues with permissions. For example, I can't save any Numbers or Pages files, as I do not have permission. It's as if it's not recognising me as a user that's eligible to save a file using Numbers or Pages. I had a similar problem with MAMP (a local server application I use to design and develop websites). I was able to fix MAMP by simply downloading the most recent version of the application from their site and installing it.

I have tried the same approach with Numbers and updating to the most recent version. This didn't work. I tried deleting the app altogether and reinstalling it. This didn't work.

I've tried First Aid on the hard drive and resetting permissions for the account. Neither have worked.

So my questions are this:

1) Has anyone experienced an account disappearing, seemingly out of nowhere?

2) Does anyone know why this occurred in the first place?

3) Why can I not edit/save a simple numbers file?