Thanks David. Thank you for the advise, in my case data.path and data.logs both were on separate disk that on a VM that I deleted by mistake so I reckon they were empty and waiting for be synced.
I suspect disk errors would have come when I attached a new disk which took up /dev/sdb.
I've run badblocks to see if I can get additional data.
should I remove cluster.initial_master_nodes from all the nodes now or wait for full recovery before thouching those settings?
Could I ask you to have a look at this: Recent unsafe memory access operation in compiled Java code - #7 by jprante. I feel it maybe the size of the indices that is causing the sync issue?