More ideas:

When using just plain
$ php userOptions.php --usage
maybe a more efficient query would be

SELECT up_property,COUNT(*),up_value FROM user_properties GROUP BY up_property,up_value;...

(if convertUserOptions.php has already been run.)

Maybe add --remove-all-unknown-options (hmm, sounds dangerous,
--dry first) that would DELETE all rows with options that have
been retired from the code.

Perhaps add a --delete-if-default,
which would DELETE all rows where an option the corresponding
$wgDefaultUserOptions[].

Bug summary doesn't clarify what's wrong or give a clear usage example leading to error with a description of the problem. Please list exact steps to reproduce and a clear description of the difference between actual and expected behavior.

Allow me to try again:
With userOptions.php, one can, for example, set users'
'rememberpassword' value, but one cannot set their 'timecorrection'
value, even though both are sitting there on Special:Preferences, and
both live together in SELECT * FROM user_properties;
+---------+------------------+--------------------------+

+---------+------------------+--------------------------+

+---------+------------------+--------------------------+
Therefore Bug: userOptions.php is unable to access some options.

$ php userOptions.php timecorrection --old='' --new='ZoneInfo|480|Asia/Taipei'
The script is about to change the skin for ALL USERS in the database.
Users with option <timecorrection> = '' will be made to use 'ZoneInfo|480|Asia/Taipei'.

Abort with control-c in the next five seconds....0
Setting timecorrection for WikiSysop from '' to 'ZoneInfo|480|Asia/Taipei'): OK
Setting timecorrection for Demon from '' to 'ZoneInfo|480|Asia/Taipei'): OK
Done.

$ php sql.php

select * from user_properties where up_property = 'timecorrection';

stdClass Object
(

[up_user] => 1
[up_property] => timecorrection
[up_value] => ZoneInfo|480|Asia/Taipei

)
stdClass Object
(

[up_user] => 2
[up_property] => timecorrection
[up_value] => ZoneInfo|480|Asia/Taipei

)

WORKSFORME?

I'll have to trust you, as my grasp of the issue is fading.

Wait, what about the wildcard I wanted?

select * from user_properties where up_property = 'timecorrection'; seems to say that '' is the same as '*' or something... bad.

Looks like it is working properly.