Note: This document is for people who want to dig into the internals and do advanced things. If you're just trying to restore something from the archive, check out Restoring from an Archive.
The .synkarchive format contains the old copies of files. It's actually a folder, but is marked as a package so that it appears as a file in the Finder, reducing clutter and allowing a helpful restoration UI when double-clicked.
Warning: The information that follows is considered implementation details, and is subject to change at any point. That said, we don't expect significant changes except where indicated, but it's possible.
As long as you have archive compression turned off, the files in the .synkarchive package are direct copies of the original files. You can copy them elsewhere, renaming them to whatever you like, and get back the original files. You can also manually delete old copies from the package as well.
If you have archive compression turned on, the contents and relationship between the files is beyond your ability to manipulate directly. As of this writing (7.0.2), you can safely manually delete old copies of the items even with archive compression turned on, but this is expected to change in a future version, so it's not recommended.