The campaign crawler will detect urls regardless of whether they are indexed of not, you should do as EssEEmily says and set up a 301 to the version with the most links if you haven't done already.

Oh and don't think just because one version isn't indexed now, it can still cause you problems down the road especially when linking is involved.

Also when setting up your redirects if you have a small number of links set it up regardless to the xxx/ version as this is the one most likely to be linked to.

Yea I agree if everything is kept the same you shouldn't see much difference but you should expect a drop and prepare for this.

That said you need to ensure the new CMS is capable of accommodation the  changes, again be well prepared.

If you intent to make changes then ensure you follow all the necessary steps and procedures that come with a site migration.

As it effected the ranking last time you can be sure it will happen again, you might want to ask yourself why your wanting to change content management systems and weight up the pros and cons, I have a site on CMSMS and I personally don't like it but each to their own