Board Thread:Naruto Discussions/@comment-30426414-20170126195341/@comment-30426414-20170127000350

Exactly, there were also other times when obito's truth seeking balls didn't negate or erase their targets, such as when tobirama grabbed one that was about to explode and teleported it back to obito, or when obito rammed through the first and second hokages with the TSB's and they regenerated shortly afterwards. There was also the time when madara stabbed sakura with a truth seeking ball but she wasn't erased and her regeneration jutsu still worked because she healed the stab wound.

This leads me to believe that the user of the TSB can dictate whether or not to use the negating and erasing abilities.