After finishing a compaction we delete the compacted away files. This is done here which uses this to get the files - we get all files starting with absoluteFilePath. Absolute file path is generated here. For 3.0 version files the filename looks like this: /blabla/keyspace1/standard1-bdb031c0ff7b11e6940fdd0479dd8912/mc-1332-big but for 2.1 version files, they look like this: /blabla/keyspace1/standard1-bdb031c0ff7b11e6940fdd0479dd8912/keyspace1-standard1-ka-2.
The problem is then that if we were to finish a compaction including the legacy file, we would actually delete all legacy files having a generation starting with '2'