Ok, so we finally managed to simulate the problem. Jackrabbit, even though it was set to info severity didn't log anything at all. Only file present in our indx directory is: "indexes_15o" and it's contents are: "_1k_105_12n_14o_16i_16m_16n_16q_16x_16z_170". Removing this file causes reindexing of whole repository and jackrabbit starts working fine again.
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