Kenny
Hi Kenny,
Some electrum servers are not 100% sync'ed (lagging), some prune their database to only contain the last 100-1000-.... tx's per address. If you connect to a lagging server, or if your address contains to much records, electrum might not show the correct BTC saldo.
However, this does not mean the funds are lost, your current server's database is just incomplete.
However, after reading your PM, i'm convinced that in your case, it was actually hacking/spyware/malware, since the inputs to your wallet were actually spent.