Syncovery works best with the option "Compress Each File Individually". That way, Syncovery (and you) can always easily see which files are on the destination. This is the native mode of operation for Syncovery, because it's heart is a "file synchronizer". It works with individual files. Not packages.
Working with individual files has many advantages, such as being able get a complete listing of all files, being able to retain a specific number of older versions for each file, being able to delete files individually, and having direct access to any specific file you want to restore.
Multiple files per package was added for specific, limited use cases only, such as one-time archiving, or regular archiving of a (smaller) set of files where each archive should contain all files.
If you really want to use compressed packages (multiple files per package), it becomes very difficult. If you delete a package, Syncovery cannot know which files it contained and cannot re-copy them. If you want to restore a single file, it will be extremely hard, if not impossible, to find which package contains it. This is just not the use case that Syncovery was designed for.
When you use packages with multiple files per package, Syncovery cannot see which files are already on the destination side. Therefore, files have to be marked as archived on the source side. On Windows, this is done with the Archive flag. On Linux or Mac, it can be done with Extended Attributes. The archive flags / extended attribute marking options are under Masks & Filters -> General Filters.
Either way, please make sure you have the latest Syncovery version.