What do you think is causing Bitcoin Core to show that available balance? Is it "confused" or caught up in a transaction history that... just doesn't exist?
This can only happen if your node is not fully synced, in your first post you said you've already synced it so this shouldn't have happened.
Try using
listunspent to see which outputs does your node thinks are unspent and then check the transaction IDs in your Electrum to see if they all exist in your history tab. If they don't that means you haven't imported one address with a bigger balance.