As a data point, I too had no problem removing my old bottom bracket and fitting a new (in my case, external) BB in my Thorn Nomad with the eccentric secured in the frame.
As Geo' cautioned, be sure to use this as an opportunity to apply fresh grease to your eccentric so you can avoid future problems with galvanic corrosion and so the eccentric can be easily adjusted to take up chain slack at some future point.
Best, Dan.