Upside of moving large files out of the way is that we won't have to try to process them again in the next round.
However, keep in mind that for small files we don't actually move the files to HBase, we upload a copy. The original is kept in place to be trimmed by normal processes.
The reason is that the normal JobTracker / Resource Manager and/or the JobHistoryServer still has access to the history file (large or not). 
When we immediately move large files the consequence is that no normal analysis through the normal UI is possible for those large files as soon as hRaven comes around, which at the moment is every 10 minutes or so.

Wouldn't it be better to simply skip the files ? Skipping the corresponding jobConf files for large history files is probably not a bad idea, although the later processing does handle the case where the history file is missing when the conf is present if I'm not mistaken.