This is a known issue, we have resolved it in dev and it will be fixed in Skuid’s Winter 15 release, and probably an upcoming patch release of Skuid Summer 14.
Pat - In the mean time, you can refresh the page and the subquery will come back. (Remember to save first). The code is not lost, just the visual…
This will be fixed in patch 5.21.6 of Skuid, which will be pushed to all orgs on the 5.21.x branch at the end of this week. If you are not on this branch, go to the Skuid Releases page and install the “Dreamforce 14” release.
This was fixed in today’s patch release 5.21.6 of Skuid, which is now available on the Skuid releases page and will be pushed to all orgs on 5.21.x during this weekend.