Ran codesign -fs – /Applications/Utilities/Boot\ Camp\ Assistant.app how to reverse it

Yep, that's kinda odd. Might be because it needs to partition a contiguous chunk, for efficiency reasons, for Windows. If that's the case, and it's got some immoveable files within that contiguous chunk, I could see it having issues.

I wonder if it would be possible to run boot camp assistant from the OS X disk instead. If you can, those files could probably be shifted as you wouldn't be booted from the 1st partition anymore.

Alternately you could create a bootable partition on an external hard-drive and do the same from a fully functioning OS X installation. Finally, the last resort would be to use a 3rd party utility to add that NTFS Bootcamp partition. I don't recommend that route.

Before OS X 10.10, you can run sudo codesign -fs - /Applications/Utilities/Boot\ Camp\ Assistant.app to re-sign the app with an ad-hoc signature.

In order to re-sign it in 10.10, you need to additionally specify the --deep command to re-sign bootcamp:

sudo codesign -fs - /Applications/Utilities/Boot\ Camp\ Assistant.app --deep

'--deep' When signing a bundle, specifies that nested code content such as helpers, frameworks, and plug-ins, should be recursively signed in turn. Beware that all signing options you specify will apply, in turn, to such nested content. When verifying a bundle, specifies that any nested code content will be recursively verified as to its full content. By default, verification of nested content is limited to a shallow investigation that may not detect changes to the nested code. When displaying a signature, specifies that a list of directly nested code should be written to the display output. This lists only code directly nested within the subject; anything nested indirectly will require recursive application of the codesign command.