1.8 Suddenly Shrouded

[MrJspeed]

I'm looking for instructions to edit my save file.  It seems just about every major KSP release results in a lot of my on-orbit engines getting shrouded.  I think it has something to do with me having craft launched with the shroud setting on, but not activated since nothing was node attached below the engines.  Everything is fine until a release adds them on.  In the case of the nukes, it's a half shroud.  I have some Rhinos and Terriers flying around with full shrouds.  

Anyone have advice on editing these out?  My prior methods of "hyperediting" replacements is not something I'm too keen on, considering some of these craft have labs with data/experiments.