I've never done this myself on the scale you prepose. However, if I was doing this,I would do the following.
Do a water change and save the waste water. At that point pull out the rocks you wish to break and do so. Place them into the removed water with full filtration and flow. If after a period of time you have no spikes in nutrients, then place rocks as you wish in your tank. It would be hard to tell (for me anyway) if you would have to re cure your rocks or not, so this seems to be the safest route to me.
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