Or is your problem more that the bigger piece is not a solid?

There are some "naked edges" around the blue piece - that means that there are some gaps there were that piece did not touch closely enough to the other surrounding objects to get fully glued together.

It also looks like there are some little slivery surface fragments in some areas there too, so possibly that blue piece did not get constructed very cleanly or something like that, that piece may need to be rebuilt and rejoined in, in order to make a fully closed solid main piece there.

Is that the area that you were asking about - are the 3 pieces then the blue piece and then other 2 ones on either side of it?

I think that's maybe what you were meaning, sorry for my confusion - it's partially joined in some areas and not in others, so that makes it select still as one object even though there are some places where it is not sealed up.

One thing that can help to see where you've got problem areas is to set up a shortcut to select "naked" (unjoined) edges, as described here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=4869.5

- Michael