Mate failure in sub-assembly

If you need to produce a drawing of the sub-assy with all its components in defined positions relative to one another, and these positions are identical when the sub-assy is used in a parent assy, then you shouldn't be making it flexible.

You only need (usually) 3 mates to fully constrain the sub-assy in the parent assy, and this should preferably be done using its front/top/right planes or origin. It sounds like when you initially added the components to the top level and mated them, that you may have created more than 3 mates between these parts and the parent assy. When you moved them down a level, these "excess" mates caused an over-constrained situation, because the sub-assy is treated as a single rigid body.

It may be that you got away with it at first, because there were no conflicts and so SWX allowed the over-constrained condition, but once you changed the geometry a conflict occurred.

It seems like you need to delete some of the constraints between the sub-assy and the parent assy - possibly all of them and start again, if necessary. You might also find you need to add some more constraints in the sub-assy to fully constrain all of its components.

John H