Mysterious indeed,
There must some something wrong with your wallet.dat file, like tampered data that got "fixed" after loading the wallet.
Did you actually mined those coins or have you bought/received that wallet.dat with mined coins from somebody else?
I also wonder same thing since i found matching 1 fake wallet.dat with contain coinbase transaction from 2009 and 2 another from 2010[1].
The thing happens in a mysterious way, when synchronizing the wallet after the years, the transactions disappear....
That will happen if sometime during those years the bitcoin was send to another adress.
In such case, Bitcoin Core would show additional transaction where the Bitcoin is moved rather than delete existing transaction from transaction history.
[1] allprivatekeys[dot]com/wallet.dat?mined=on