Let $R$ be a regular local ring of dimension at least 2, and let $U$ be the complement of the closed point in $\mathrm{Spec} R$. Given a polarized abelian scheme over $U$, under what hypotheses can it be extended over the entire base? 


In the mixed characteristic or equicharacteristic $p$ setting, some conditions are needed - an example over $W[[x,y]]/((xy)^{p-1}-p)$ due to Raynaud-Ogus-Gabber is described in 
a paper of de Jong and Oort, "On extending families of curves", Journal of Algebraic Geometry, 6 (1997), pp. 545--562, apparently illustrating some errors in Faltings-Chai. Is there some standard fix that makes such extensions possible?



Extending abelian schemes
A false theorem was given in Faltings and Chai in the end of the section V of their book, but as you said Raynaud found a counter-example. Vasiu and Zink have since worked on the subject :


<http://www.mathematik.uni-bielefeld.de/~zink/ValidusJ.pdf>


