When you re-run the process flow, the prompts should show again -- as long as the prompts are correctly associated with the query (which they should be if you selected them via point-and-click). If you referenced the prompts in the query simply by typing in the macro variable, that isn't good enough.
You can also check the query properties (right-click on the query node, Properties) and make sure that the prompts you need are in the Prompts list.
If this isn't working for you I recommend checking with SAS Technical Support.
Chris
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