EDIT：
You should use the first one, i.e. "The following three major challenges have to be met if a family business is to flourish for 100 years and more."
Since a family business to flourish for 100 years and more is not impossible, you should be using Future Real Conditional explained here: Future Conditional Forms | ENGLISH PAGE
Future Real Conditional
FORM
[If / When ... simple present ..., ... simple future ...]
[... simple future ... if / when ... simple present ...]
Notice that there is no future in the if- or when-clause.
An example:
I am going to read if there is nothing on TV.