We experienced a similar error yesterday. We are running MDex version 6.2.2.
Upon investigation, we found that the baseline update had failed, since we had attempted to load zero records. (Turned out that our extract process failed due to a deadlock.) Even though the dgraph was still working smoothly, my guess is that the zero record load somehow wiped out some dimension references, causing the 'Dimension refs parsing error'. The problem was corrected once we reran the baseline update.