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The database stores a list of transactions in those zip files, describing changes to the contents of the main database file, named 000000000... and the database compaction process consolidates all of those changes and writes out a new copy of the main file. So, when you delete the action, a new zip file gets created with contents saying that the action id erfkjh234xdfed has been deleted, and when a copy of OmniFocus reads that file during a sync, it knows to update the display to not show you the "deleted" action. However, it is still present until all of the clients of that database consolidate that action into the main file, at which point it is removed. That is why your database does not necessarily immediately shrink when you remove a big attachment.