Steps to replicate the issue (include links if applicable):

Use the userOptions.php script is used with --delete --old '' (delete all rows with up_value equalling an empty string). A specific example:

urbanecm@deployment-mwmaint02:~$ mwscript userOptions.php --wiki=enwiki --delete --old ''  --fromuserid=11941 --touserid=11943 --nowarn 'echo-subscriptions-web-reverted'                                                                           
Done! Deleted 1 rows.
urbanecm@deployment-mwmaint02:~$

What happens?:

All rows with matching up_property were deleted.

What should have happened instead?:

Only rows where up_value = '' were deleted.