Crypts usually melt to adjust to new conditions (dispose old leaves, grow new suitable ones). Most often to adapt from emersed to submersed conditions. Changing water or topping up should not cause a melt, unless you are stirring up a lot of dirt or doing a lot of replanting or uprooting.
So far, I've not have problems with crypts melting after as big as a 50% water change.
From your post, I can't figure out whether you are asking before you try water change from tap or whether you've done so from tap and experienced a melt.
In the former case, try a change from tap first and see if your crypts melt. If you are really worried, then use water aged in a pail.
On the latter case, let the leaves re-grow and water change again. The crypts may have adapted to the new water source.
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