Gotta see a pic of this, can you put one up? Yeah a lot of roots end up on the bottom, but the idea is to add soil volume around the whole root mass so it can develop both out and down.
Generally it's inadvisable to transplant or do anything major after commencing flowering. Get them all healthy and trained to your satisfaction, throw the switch and leave them alone.
What did you even gain by putting them in a larger pot with not enough soil anyway?