I have the same problem, but on Eos. Architect remains floating in the air after the 2nd conduit is destroyed and it's supposed to move to the final battle location. No trouble on my first playthrough, but I faced this issue on my new game+ playthrough. Thus far I am only at the architect on Eos and none of the following planets, so I can't confirm whether this issue is isolated to the Eos architect or not.
Edit: forgot to mention, I could not get the swap squad member+save/load workaround to work.
