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We have two servers - Production and Edit. The Production site is 99% read only and all edits are performed on the Edit site. We use Content Deployment to move the changes from Edit to Production on a nightly basis. The 1% of editing that happens on the live site happens in lists that are NOT migrated ever. When setting up the deployment job, we followed this guide by Stefan Goßner.

The job has been running for 9 months with only a few issues now and then. But, strange things are starting to happen more frequently. This morning (maybe not the first time) this warning appeared

[12/22/2010 5:11:13 AM]: Warning: The list item with Id 0d7a5cb7-2222-4715-930b-022a8f7a6041 cannot be deleted because it does not exist in the destination site collection.

A Google search reveal nothing useful. Should I be concerned? It seem that Production and Edit are getting out of sync. It would be very difficult to do a full content deployment again. Is there any way to 'refresh' all content without doing a full migration?

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The official line on content deployment is that you shouldn't touch the target site. I realise that isn't very helpful in your case. Content Deployment is not always such a good solution for authoring as it first seems (although much improved since the SP2007 RTM). Editing on the production farm, using versioning and the publishing workflow of course, is often preferable.

In your situation I think I would be inclined to soldier on rather than do something drastic, but work on the assumption that something might go horribly wrong at some point. Make sure all your backups are working, and be prepared for the possibility of wiping the target site and re-deploying the content. If possible build a test farm to verify this will work and get a feel for timescales.

Consider switching to authoring on the production environment at some point in the future, unless there is a compelling reason to have a staging server. You can still have a web-front-end dedicated to authoring with the single farm approach.

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I had the simular issue. I ended up deleting the content DB, recreating a Content DB, and running a new content deployment job to populate the site.

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Have you tried looking in the recycle bin of the destination site to see if the list item is there? I would try this route before attempting any other strong measures

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