I haven’t tried using the refresh from inside the query builder.
But I can see the table/sub table correctly in the DB manager.
Will try that as well, although not very hopeful about it. 
Bumped into this again today. All tables need to be available when creating a join.
I have been experiencing this issue as well. Some subtables are not available in the list of database tables for a JOIN.
Fixed in Wappler 5.5.3
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