I feel that any personal numbering system can safely be removed, with a public bulletin board comment that it was removed for lack of documentation.
In the case of John Smith 1, 2, 3, etc., I think you might want to add a comment of why the number was removed (Suffix: Preferably, this should only be used for the Suffix at Birth. For example, Jr. and III. https://www.wikitree.com/wiki/Help:Name_Fields#Suffix) and ask for documentation that the name included the number at the time of the person's birth.