Once you sell items at a trading city, your ships sail back with silver on board.

In the case of trading, when you buy items, silver is instantly used. 

But when you sell items, the silver is not given until your ships have arrived at the dominion. 

When the ships arrive, you can only get the amount that your Depot can hold.

In short, if the silver you have earned exceeds the amount you can hold, 

the rest will disappear.

Therefore, before your ships return, make sure to either upgrade your Depot to hold more silver 

or use the silver so that you can receive all the silver for your hard work.