As i suspected after 3 days of trying. Issue was in old wallet.dat file. It didn't have some hidden new master keys or private keys. The amount of displayed addresses didn't change. But after i used latest wallet.dat all transactions showed and funds was taken out swiftly because now i need new wallet due to, to many manipulations trying to fix it.
Problem is Electrum picked up that new hiden addresses and send funds to them. And i still cannot see any new addresses or keys in my Core. They came in as brand new addresses i never seen before. But non the less it was received.
Also another issue that stands, is electrum Crashing when trying to display private keys from imported wallets as well as from GUI or Console after updating to 4.0.2, alltogether or single. Also forever disabled buttons to sign or broadcast. Unable to send funds through console. Seems it cannot connect to servers well enough to process transaction. I would recommend for people using Electrum to switch to core. To many bugs in Electrum. So much again for Newbie friendly easy wallet Well i am happy now finally i can sleep well.