You can upload them again, you can use files directly from /export/mirror/... .
The problem is that some other packages might have been removed from some catalogs. Not your packages - some other packages. These need to be uploaded again as well. Perhaps the atom feed contains this information. I have read the code multiple times and I don't see a bug. I an suspecting things like caching in the ORM, or parallel runs. I have recently added more logging to obtain more information. But the issue hasn't been triggered since, until now. I am now on vacations until the 17th, I will look at the logs then. Until that time, please try to identify the missing packages and upload them again. Sorry for the inconvenience! Maciej
