The honeycomb-lattice ruthenate Li$_2$RuO$_3$ is made heavily Li-deficient by chemical oxidation by iodine. The delithiation triggers a different phase Li$_{2-x}$RuO$_3$, the D-phase, with superlattice. For the first time we disclose the magnetic and structural properties of the D-phase in the dimer-solid state. The low temperature magnetic susceptibility and the bond lengths indicate a bonding configuration consisting of both Ru$^{4+}$-Ru$^{4+}$ and Ru$^{5+}$-Ru$^{5+}$ dimers.
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