There are instructions at the bottom of Minor Updates within 3.3.x to deal with a couple of files in the store directory if the previous attempt failed or was abandoned to try another method. 

Unfortunately these same instructions are missing in the subsections for the several update paths, i.e.  

• Full Package
• Changed Files
• Patch Files

See https://www.phpbb.com/community/viewtopic.php?p=16041106#p16041106 for details on how this confused an admin doing an update.