This looks like it is the write cache. Workaround is to disable the write cache in HdfsDirectoryFactory: solr.hdfs.blockcache.write.enabled=false
Index is not actually corrupt on disk, you can restart on it fine.
Grabbing the updated BufferStore stuff from https://issues.apache.org/jira/browse/BLUR-294 seem to fix this issue.
Commit 1561751 from Mark Miller in branch 'dev/trunk'
[ https://svn.apache.org/r1561751 ]
SOLR-5666: Using the hdfs write cache can result in appearance of corrupted index.
Commit 1561752 from Mark Miller in branch 'dev/branches/branch_4x'
[ https://svn.apache.org/r1561752 ]
Move issue to Solr 4.9.