I have seen this discussed (perhaps in the FAQ). You have the option. Repair or fortify. If you fortify then the breach(es) remain.
hmmm, that doesn't make any sense either...either you fortify and build all new walls or you don't-
we play like this:
YES - you can fortify but have to pay one extra gold for each breach, since it hinders/complicates proper building (debris and so forth)
this is our interpretation/modification on the rules and it makes sense for us... hope that helps