To update a file in a .appv package, open the .appv in the sequencer and select the "Edit Package" option and click "Next".
Expand the path to the file you want to update and right-click and select "Delete".
Right-click the folder above and select "Add"
Browse to the file, select it, click "Open".
Click "OK" to make a new VFS mapping. Choose File > Save and save your package.
If you have the original package and rename it to .zip from .appv and get properties on your file, and do the same on your new version of the package (after making a copy of it) you should see that they are different and you have a new file in the new version without having to "Update" the package; avoiding capturing additional garbage that happens when you update an application.