Mysql – Tokudb 5.7 [Warning] The partition engine is deprecated and will be removed in a future release

If I understand it correctly, there can be only one config file. But mine ends with

#
# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/

and so it is directly responsible for "merging" those additional ones into itself.

The !includedir directive is covered in the manual https://dev.mysql.com/doc/refman/5.5/en/option-files.html which states:

There is no guarantee about the order in which the option files in the directory will be read.

So it probably depends on the OS and filesystem but you should not depend on it anyway, even when it seems "stable" for now.

I sugget using the !include directive instead and maybe a different folder for those config files where the order matters.

I want to increment a counter in the selected row, but only if the row's status column is ACTIVE. If it is not ACTIVE, then I just want to release the lock without an update so other threads/processes can read/write that row.

Don't have the SELECT; simply do

UPDATE tbl
    WHERE ...
      AND status = 'active'

The UPDATE will either change the row or do nothing.