For simple file aggregates in a package, the child node jcr:content or vlt:definition is not correctly overwritten.
Example
State in repository:

+ content
   + test
      + 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.

Environment

AEM 6.3.1.2 and below.

Cause

This is a known issue fixed by JCRVLT-177 in Jackrabbit FileVault 3.1.40.

Resolution

Install AEM 6.3 SP2 that will update the bundle Jackrabbit FileVault to version 3.1.42.