At this writing (2014 July) we're still using the original root KSK as was used to sign the root zone initially in 2010. BIND 9 will do the right thing in accordance with RFC 5011, if the root zone operators do. BIND named stores the root key as received and validated from one or more root servers in its managed key database. As long as your server is up and running and connected during the RFC 5011 rollover period, you should be fine.
Of course, if the root zone operators fail to adhere to RFC 5011 procedures in their KSK rollover, we do not know what to expect.
If your server misses out on the rollover period for some reason, including an initial install or activation of an outdated copy of BIND after the rollover completion, this will take just a bit longer. See below about bindkeys-file.
Note that here, the word "outdated" might mean simply that the rollover took place before ISC was able to release new BIND versions. If/when the root KSK changes, ISC will strive to release an update to all then-supported BIND versions, and this update will contain the new trust anchor.