Appication upgrade in sharepoint c#

Hi there I have custom visual studio project done in vs2010 c# . This has user controls, event receiver , ghosted pages and especially list definitions and list instances.
This project has been compiled and put in production. The users are using my application.
Now we need to deploy another version due to bugs encounted by users and I am worried I might loose existig work done by the users. What is the best practice to ensure upgrade of custom applications are ok . Is this correct when you deploy list instances to your project , the data is wiped ?

Thanks kindly