For simple file aggregates in a package, the child node jcr:content or vlt:definition is not correctly overwritten.
State in repository:
+ thumbnail.png [nt:file]
+ jcr:content [nt:resource]
+ dam:thumbnails [nt:folder]
In the package you have the filter
< workspaceFilter version="1.0" >
< filter root="/content/test" />
< /workspaceFilter >
And the package content consists of only the binary file /content/test/thumbnail.png.
Once you install that package it will not remove/recreate /content/test/thumbnail.png/jcr:content and also leave the child node dam:thumbnails in place.
This is a known issue fixed by JCRVLT-177 in Jackrabbit FileVault 3.1.40.