The Sovereign damaging problem is something that I've only noticed in SP, and it's occurred regardless of which Sovereign-class I use - I have made a patch that will increase the hull radii of all Sovereign type ships in the modification and hopefully address this.
The batch file is set to delete these folders and ALL of their files, subdirectories, and subfiles; the batch file is however scripted in terms of Windows 2000 and XP DOS commands, which may be different than those in earlier operating systems.
For example, the older operating systems use "deltree" to delete a directory and all of its subdirectories, whereas 2000 and XP use "rmdir /S" to accomplish the same thing. If you're using an older operating system then the batch file may not work - I guess I just now figured this out.
Delete the following folders and then reinstall the modification:
"scripts/ships"
"scripts/Tactical/Projectiles"
"scripts/Maelstrom"
"data/Icons/Ships"
"data/Models/Ships"
"data/Models/Bases"
"data/Models/SharedTextures"
"data/Models/Misc"
"sfx/Explosions"
"sfx/Weapons"
-CR