When I use the update on some songs it says there corrupt and deletes them. I have found that some of the songs run fine but it deletes them. Is there a setting that will leave these so-called corrupt files also where does it put them it says sub folder.

No, there is no setting to leave a corrupt CDLC in your song collection.  The reason the CDLC seems to play fine may be because you have not played the corrupt arrangement yet.  CDLC have multiple arrangements and any one of them could be corrupt.  CFSM moves the corrupt CDLC to the 'corrupt' folder because if you did play the arrangement that is corrupt it could end up corrupting you game save.  So to be safe it is removed from the collection. 

 

It would be a good idea to contact the CDLC charter and ask them to fix their corrupt CDLC.  If you can't  contact the original CDLC charter then you may be able to repair the CDLC yourself by unpacking and repacking it with the Rocksmith toolkit.