Flash the newer version of ROM over the old one on ART environment
It should be identical to flashing when Dalvik is enabled. If the ROM cook packaged up everything correctly, you should be able to "dirty-flash" the nightly builds over the previous ones (assuming you are staying on the same ROM channel.)  I would confirm with the ROM author though.

On the topic of wiping caches, the CyanogenMod's installation instructions specifically state:


  Contrary to popular belief, there is no need to wipe ANYTHING when you
  update CM. This includes your cache partition, your dalvik cache, and
  your battery stats. While wiping these won’t hurt anything, you can
  increase the time it takes to boot up CM after you install the update.
  Android is smart enough to manage both your cache and dalvik cache
  without you intervening, and wiping your battery stats does absolutely
  nothing to help with your battery life (the file is only used to
  provide the raw information to provide the stats and graph in Settings
  -> Battery) – it is actually wiped automatically every time your device is charged to 100%.


Of course you should always have a recent backup via recovery in case things start to go wrong.