Thanks this answered my question. The paid die is rerolled again after being used if one uses it to pay for the crystal as required by the action cards.
I will rather clarify: you can use only one die from the source, unless cards explicitely allows you to use or manipulate extra mana die.
The fact the card requires you to pay mana DOES NOT allow you to use extra mana die. You can use mana gained by any way for it (for example from glade, from another card, unit or skill token, or even from a crystal, although it does not make sense in most cases), including mana gained from a mana die. However, if you use a mana die to pay for the Crystalize effect, you cannot use another die from the source that turn.