Recently we have had issues with Favorites disappearing. After short investigation we have found that the
"application_name.Meta" files which get created automatically for each application store a list of users ("domain_name\username" in our case) who added the application to favorites. Those files are located in the same folder as the distributed ".qvw" files when using a publisher.
In our case we had problems with favorites not working when we transitioned to a new domain. All references to the old domain in the .Meta files were not updated, hence the problem. I have not found a good way of editing the meta files though.
As far as your issue, I'm guessing during your manual process you must be getting rid of or replacing the .Meta files with new ones...
I think you need a little bit of more information, the .meta and the .share are files that contain information of authorization, attributes, licenses etc. these files do not are erase, perhaps the files are in the trash, if you restore this files I think that your environment work without problems only in the case that you can find these files.
I leave you more information of this files.
File where are stored the QlikView licenses, these files are important because if they are deleted, usually these files are important, because they contain a user license
AccessPoint attributes, pre-load options and authorization (Document Metadata Service – that is, DMS – mode only)
Bookmarks, Sheet objects, including charts,Reports, annotations
Contains everything: Load script, User Interface, data, associations, security etc. This is what you and your end-users will be working with.
QlikView Data File Contains a single internal table, loads extremely fast.