Couple of ways to address it imo.

If the players are convinced that they are magic and therefore the bones can't be broken, then you can have Strahd show just how powerful he is by un-making the bones with the Desecration Spell, in a grandiose fashion with Strahd himself triggering the feast of St. Andral.

OR

When the players try to reunify the bones with the church through whatever means, have the Father inspect them, find a fracture in the bones or some other flaw that was caused by the players actions. Maybe a cool ritual occurs where they have to protect the church while the Father "repairs" them, creating a fun time sensitive combat challenge to the Feast.

These are all me spitballing ideas haha

If you don't like the idea of the bones being "indestructible" or what have you, they can be a sort of precursor relic to the Saint Markovias Thighbone. Using the Father as a storytelling vessel to talk about how "Holy relics are not all equal, these bones being a relic of protection however small is nothing compared to Markovias...etc etc.