I’m still not sure what this does 
At the moment it really doesn’t matter since it is will probably not fix it. Because even if a password login for root is disabled, you should be able to try to login. For example,
$ ssh root@test.vir
root@test.vir's password:
Permission denied, please try again.
root@test.vir's password:
Permission denied, please try again.
root@test.vir's password:
Connection closed by 192.168.9.17 port 22
At first you still need to find out, if you can connect to your Pi over ssh by port 2222. If possible do not use root, use a normal user. Do not use sudo. simple ssh -vvv -p 2222 username@IP .
Also verfiy if the IP you use is correct.
I’m looking through the contents on the SD card on my Raspberry Pi in Windows (as it is very weird on Manjaro) and they aren’t what they should be. I cannot find some of the files I had created on it and some of the edits I made are missing too. I am unsure why it is like this, perhaps looking through the contents on linux does something to it or it may as well be my SD card reader because it is quite cheap.
I was willing to ask for help as a means to learn if a reocurring issue ever came across again. But I might as well just make a clean install on the SD cards.
You won’t be able to read the Ext4 partition from Windows, you will only be able to see the boot partition.
Checking it on linux and it is different. But, I’ll just do a fresh install on the SD cards, it will save the time and hassle.
Thank you everyone for trying to help, I really do appreciate it 
Be very careful what you do with Ssh… You are basically punching a hole though your firewall. If you are going to exposed it to the outside world.