I download from the service and open the dataset and see the message "There are pending changes in your queries that haven't been applied". If I click apply changes, all the tables in the dataset dissappear. The data set becomes empty.
I was going to start over by opening the mqueries and recreated the data set. But no.
When I right click a table ... and select edit query I get the dialog "No Query Found" , "Please refresh the model to discard any stale data"
The data set it working. I see the data. The data set refreshes in the service. The data set has parameters and is connected to power bi data flows.
My situation was simple: i loaded 2 objects from SalesForce and then tried to load 3 more (due to lack of memory, the action was stopped).
Then i could not for the life of me, delete the tables.
So i deleted all connections that related to those 2 tables, then i clicked Edit Query (from one of the tables i wanted to delete), then on the left hand side you get a list of all the pending queries, and i found the 2 loaded ones and the 3 that stopped. I right clicked on each of them and deselected "Enable Load" and i was prompted with the message that it will not include the tables in the next refresh (i singed Halleluyah)., then i hit Close and Apply, then i clicked apply changes (once i got the yellow message) and behold: they were gone.
So this was the story of my thriller, albeit a simple one (i did not do any connections or editing on them). But disabling the "Enable load" function should work.