The car is now fully painted and everything put back together

But the fixing bolts to the underside of the Plus side skirts are in bad shape.

Can anyone recommend the best way of securely re-fitting the skirts? Is it just a case of bonding them on with plenty of mastic?

If it was me, I would use Sikaflex, having similar before.

The only thing with fully bonding them on is that they would be difficult to remove if required later on.

But then again, with the bodywork newly painted behind the sills, it is unlikely that they will have to come off again?

Some people recommend Tigerseal for jobs like this. It is incredibly strong once set (it sets like hard rubber) so would be very hard to reverse if you wanted to get back to clean paint / not break the skirts removing them.