I agree - loosing everything is often the reason why people stop playing.
But banks that aren't linked could have something like a hidden cellar, safe spots outside the city to hid stuff, ...
Ingame that could look like a bank system where you have a part thats "safe".
If you have to much stuff the part in the "not safe area" is lootable.
In a case like this it would be your responsibility to bring the stuff to a safe place like your own house.
Maybe part of the city development could be to create "more safe space"?
When you loose a siege you could it explain as "An NPC takes the stuff thats in the safe part of the bank and brings it somewhere during the siege". The owner could get a map with information where to find the stuff.
Then you can get this stuff thats somewhere hidden outside the city.
Maybe add a timer (days / weeks) before everyone has the chance to find the hidden stuff?
Because I don't think it would be possible to get a lot of stuff out of a city that an enemy controls.
And owning stuff that you can't access is the same as losing the stuff.