Ship Plugin Issues - deleting ships from the game menu

[Gorandius1256]

Using the search feature I found nothing on here that seems remotely similar to this so here it goes:

I am attempting to install replacement ships for the stock KM2011.10 models and am editing my menus to be a little more compact (Example below).  However, whenever I delete the plugin files for any stock KM ships in the <BCDir>/scrips/custom/ships, I go into quick battle and the ships are still in the menu.  Is there some coding in KM that prevents me from deleting these ships from the game menu similar to the stock ships?  If so is it possible to remove them completely so I can move them (their replacements) to the destination I desire.

Example of My desired Menu Tree:
Federation Ships
-->TOS Era
----> Constitution Class
-------> USS Republic

Don't know if this'll help, but here is a link to my console report:
http://i254.photobucket.com/albums/hh120/gorandius1256/Conoslereport.jpg

[Defiant]

Of course there is no extra code.

Make sure you delete .py and .pyc

[Gorandius1256]

I don't see any .pyc files in my plugin directory.  Is there anything in my src folder I should delete?  Or am I missing something simple here that will me feel ridiculous once I figure it out?

EDIT: Okay, I solved the issue.  My UAC settings backed everything up to a hidden folder automatically.(C/User/appdata/Local/VirtualStore/Program Files (x86)/Activision/Bridge Commander) and whenever I launched QB, the game called back those scripts because I had deleted the other ones.