I'm not sure if there's an easy way to deal with this but when I updated from
XF3 -> XF4 x11-links didn't complain but it was broken otherwise as it
was missing critical includes, etc.

Now the case could be made you should reinstall all your X packages on an 
upgrade like this, but if they work...

Anyways, having some sort of package check in x11-links that can complain it's
out of date would probably be good.

James