Is it possible bitcoin-cli is accessing/editing a different wallet than Bitcoin Core GUI?
No, bitcoin-cli does not access anything. It interacts with bitcoind or bitcoin-qt so it "accesses" whatever the running instance of one of this is using.
It is possible that bitcoind is accessing a different wallet from bitcoin-qt. The first time you ran bitcoin-qt, it should have asked you to choose a data directory. If you have changed it from the default, then your wallet file and all of the blockchain data will not be in the default datadir. However if you start bitcoind without the
-datadir option, then it will use the default datadir which means that it will be using a different wallet and downloading the blockchain again. To check your datadir, open bitcoin-qt and go to Help > Debug Console > Information. It will say what the datadir is. If it is not
C:\Users\<username>\AppData\Roaming\Bitcoin, then you are using a custom datadir and when you use bitcoind it will not be using that datadir.
If you are using a custom datadir, bitcoin-cli will need to have the
-datadiir option set so that it also uses the same datadir to get the information it needs in order to access Bitcoin Core's RPC server.