Did you also remove the update from the update group (2012) or update deployment (2007)? I don't think not doing so should cause the issue you are seeing, but since you didn't mention doing so, I wanted to ask.
J From: [email protected] [mailto:[email protected]] On Behalf Of Daniel Corkill Sent: Sunday, June 30, 2013 11:11 PM To: [email protected] Subject: [mssms] Problem with software update package seemingly corrupted This has happened twice now so I want to try and get to the bottom of it... About a month ago I removed an update from our software update package (I use one yearly package) and then refreshed the package after doing so. Following that I had reports from users of updates not downloading. Reviewing the DataTransferService.log its stating it can't find certain updates on the DP and it's unable to download the manifest. Anyway, that night I selected all the updates in the package and performed a content refresh followed by an update to all DPs and this got it going again. Now, after deleting another update from the package a week ago and refreshing DPs I've got systems with the exact same problem. So I'm going to have to go through the whole content refresh again tonight. Does anyone know what could be going wrong here? Am I not removing updates correctly? The package currently contains 319 updates. Daniel.

