I would err on the side of simplicity and treat repairing a destroyed holy site in all ways the same as creating a new holy site.

The rules left the question open on whether repairing is different to building from scratch. However, granted that the might investment works the same way between building and repairing, there's a precedent for all the other mechanics to follow a similar pattern.

Of course, if we want to lay down a new ruling as errata, I'd be willing to hear cases. It might be fairer to relax or remove the timer when repairing holy sites. I mean, that's the best case I can think of for repairing existing holy sites being its own mechanic.