The database files that are being updated are always there.
So, all this update does is replace the database files, with the newer version.
What is actually still in the database info files, is not changed much, if at all.
The repositories are constantly adding or deleting stuff.
The database files are used to tell the Puppy Package Manager (PPM) what is in the different repositories.
These database files are static and only get updated with changes, by using PPM update database or by the auto update, that is in /root/startup/
With PPM, it is easy to forget to run PPM update database, before you use PPM to download and install something.
With old database files being read by PPM.
Good chance the download and install will not be good or miss something, that is now needed.