What could be possible reason for this,
Could not delete list instance ‘Lists/Documents’ from server.
Could not delete list instance ‘Lists/Fruits’ from server.
Deployment conflict resolution for one or more items failed. See the Output Window for details.
Related Post is here Deploy feature error – my own mistake
Have you tried Deleting the list with PowerShell? You’ll probably get the error message that Visual Studio received.
Feb 2 ’15 at 13:03
I have 100s of websites with this list using same template, going to delete all of webs
Feb 2 ’15 at 13:15
VS won’t do the cleanup on that scale, it’ll target only the site you set as the Deploy target so you’ll need the PowerShell anyways, then. I might not have understood your comment completely, was it an objection or your plan of action?
Feb 2 ’15 at 13:18
Don’t enough rank to just comment. Put in your feature deactivating code to “try” to delete the list instance before the content type is removed. When you remove the content type and list definition, the list instance still stays in the content database.
Also, as a developer, PowerShell is your best friend. It uses the same SP object model.