Hi Everett,
Thank you for your answer. I deleted the 1 and 2 directories, renamed 2 to 0. And restarted my cluster. And it worked. Thank you for your time 
What is weird is that on the third node (i'm running a three node setup) the actual current indices resides in directory 0 while directory 1 contains legacy indices. The second node is ok though (only 0 directory).
So I'm wandering how could elastic even handle data and know which directories are the good ones across nodes.
I'm running elastic inside a Docker, One single instance per node. This problem happened after a hazardous shut down that i've mentioned here : Elastic inside Docker loses docs when shutdown while bulk indexing
Thank you for your time.