We present the first ever X-ray data taken of an intermediate polar, FO Aqr, when in a low accretion state and during the subsequent recovery. The Swift and Chandra X-ray data taken during the low accretion state in July 2016 both show a softer spectrum when compared to archival data taken when FO Aqr was in a high state. The X-ray spectrum in the low state showed a significant increase in the ratio of the soft X-ray flux to the hard X-ray flux due to a change in the partial covering fraction of the white dwarf from $>85%$ to $70^{+5}_{-8}%$ and a change in the hydrogen column density within the disc from 19$^{+1.2}_{-0.9}times 10^{22}$ cm$^{-2}$ to 1.3$^{+0.6}_{-0.3}times 10^{22}$ cm$^{-2}$. XMM-Newton observations of FO Aqr during the subsequent recovery suggest that the system had not yet returned to its typical high state by November 2016, with the hydrogen column density within the disc found to be 15$^{+3.0}_{-2.0}$ cm$^{-2}$. The partial covering fraction varied in the recovery state between $85%$ and $95%$. The spin period of the white dwarf in 2014 and 2015 has also been refined to 1254.3342(8) s. Finally, we find an apparent phase difference between the high state X-ray pulse and recovery X-ray pulse of 0.17, which may be related to a restructuring of the X-ray emitting regions within the system.
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