I noticed the tweet said he's doubtful for Japanese Nationals so I would think sadly he won't be at CoC.
He was scratched for CoC as of the second to last update to the ISU GP assignment list.
And as as he was not a host pick, many of us are frustrated that a replacement was not announced at that time, or in the most recent update last Friday.
http://static.isu.org/media/1001/gp_men_16-11-11.pdf

He fell on his shoulder, couldn't finish his program, couldn't even stand up straight when he got off the ice. Hope it won't be too serious...but I guess Jiri will be the new champion by default?