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X-ray observations of the optically selected $z=6.025$ QSO CFHQS J164121+375520 (hereafter J1641) revealed that its flux dropped by a factor $\gtrsim7$ from 2018, when it was a bright and soft X-ray source, to 2021. Such a strong variability amplitude has not been observed before among $z>6$ QSOs, and the underlying physical mechanism was unclear. We carried out a new X-ray and rest-frame UV monitoring campaign of J1641 over 2022-2024. We detected J1641 with Chandra in the 2-7 keV band, while no significant emission is detected at softer X-ray energies, making J1641 an X-ray changing look QSO at $z>6$. Comparing with the 2018 epoch, the 0.5-2 keV flux dropped dramatically by a factor $>20$. We ascribe this behaviour to intervening, and still ongoing, obscuration by Compton-thick gas intercepting our line of sight between 2018 and 2021. The screening material could be an inner disk or a failed nuclear wind that increased their thickness. Another possibility is that we have witnessed an occultation event due to dust-free clouds located at sub-pc/pc scales, similar to those recently invoked to explain the remarkable X-ray weakness of AGN discovered by JWST. These interpretations are also consistent with the lack of strong variations of the QSO rest-frame UV lightcurve over the same period. Future monitoring of J1641 and the possible discovery of other X-ray changing look QSOs at $z>6$ will provide us with precious information about the physics of rapid supermassive black-hole growth at high redshift., Comment: Accepted for publication on A&A Letters