Question

If I look in the database settings of my database (with SQLite Manager) I have a freelist_count of 16. According to this source the freelist count is

the number of unused pages in the database file

What is meant with unused pages and why are there unusued pages? Is it bad to have a freelist count of greater than zero? What can I do to reduce the number to zero?

Answer 1

From SQLite FAQ:

(12) I deleted a lot of data but the database file did not get any smaller. Is this a bug?

No. When you delete information from an SQLite database, the unused
disk space is added to an internal “free-list” and is reused the next
time you insert data. The disk space is not lost. But neither is it
returned to the operating system.

If you delete a lot of data and want to shrink the database file, run
the VACUUM command. VACUUM will reconstruct the database from scratch.
This will leave the database with an empty free-list and a file that
is minimal in size. Note, however, that the VACUUM can take some time
to run (around a half second per megabyte on the Linux box where
SQLite is developed) and it can use up to twice as much temporary disk
space as the original file while it is running.

As of SQLite version 3.1, an alternative to using the VACUUM command
is auto-vacuum mode, enabled using the auto_vacuum pragma.

There’s nothing bad in having some free pages, unless they take significant amount of space. It is up to you to decide where ends the “nothing bad” and starts the “significant”, depending on the needs of your application.