Hi Katy:

What version of LabKey are you using? I wonder if you are hitting this issue, which was fixed in version 24.3, as well as maintenance release 23.11.11.

Issue 49511: Setting lookup to custom query shows "Error: Lookup target table does not exist."

In addition, if you're on any version lower than 23.11.11 now, you should upgrade to the latest maintenance release of either 24.3 or 23.11 as soon as possible because of the security update described in this other post.

--Molly