I'm trying to do a deploy in a new environment for the first time, and I'm getting the error "Duplicate Sitecore ID's found in files sitecore\system\Settings.item and sitecore\system\Settings.item." This is a standard Sitecore item, and it's in TDS because a child of it was modified, but the IDs are the same when I look at the comparison chart. I can do a "sync with Sitecore" operation just fine, but I'm not sure why a deploy would complain about this instead of just skipping it, since there's no changes.
I have got issues like that before and most of times there are two items with same name and Id. Please check through the content editor if you see a duplicate item sitecore\system\Settings.
If this is not the case, did you recently update your TDS to a recent version? If so please check this (Duplicate item errors when syncing a TDS project)
You should focus on solving the issue rather than setting the item to stop syncing to TDS.
I hope this helps.
Check the TDS csproj file for multiple instances of the item. I've seen this happen when items are added and moved and synced again and the parent gets duplicated in the project.
Make sure that the deployment properties are set correctly: From your TDS project, right-click on the 'system' node and open the Deployment Property Manager.
The system node should be Item Deploy: Once, Child Item Sync: None. This will prevent TDS from attempting to sync all of the children under 'system'
The Settings node can inherit from system (parent).
Custom folders under Settings should be Item Deploy: Once, Child Item Sync: All Children. Child items can inherit from the parent.
Item Deploy: Once will cause TDS to check for the presence of an item prior to adding it to the destination environment and skip it if it already exists.
This is what I have and this gets deployed every day without incident: