Probably this could just be a glitch since as you've mentioned that ZIL is currently upgrading and the status of your wallet has been affected by it. A version of Atomic update could also be a thing here, check out if they've got some new release and update it but if there's none, then we can conclude that it's just an upgrade matter so wait until it's finished.
Yes I wrote to Atomic support and they told me that my coins are safe in the blockchain and I checked the link of my ZIL address at stake.zilliqa.com and the coins were there,they advised me to upgrade the wallet also and they pointed out to be an internet connection issue which is not at all a problem,I have a very fast connection at home.Also I am not hacked and if I were the hacker would leave trace as the transaction that he would have taken my money would be there in my wallet in the transactions tab.I will upgrade the wallet today and see if there is anymore problems but the good thing is my coins are safe.In Linux we are usually much safer than in Windows regarding hacking although lately a lot of malware is attacking Linux devices also.