How can I differentiate the words a big chocolate-chipped pie ㅡ a pie that has big chocolate chips ㅡ and a big chocolate-chipped pie ㅡ a big pie that has chocolate chips.
I don't think that you can unambiguously communicate either of those ideas using that phrase. If you want to sound natural, big will always be listed as the first adjective. My recommendation would be:
a pie with big chocolate chips
for the first meaning, and
a big chocolate chip pie
for the second meaning.
To add some clarification - again, this has to do with sounding natural in English. We have apple pies and coconut custard pies, but not appled pies or coconut custarded pies. The reason for this is that the descriptors for the type of pie are not simply adjectives, but rather noun adjuncts. Chocolate chip functions in the same way. Chip is the adjunct noun modifying the type of pie, and chocolate is an adjective describing the type of chip.