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Srinath, did you find a way to resolve this? I have a similar problem in that any new queries I create in Access are not visible to Alteryx. When I try to refresh the cached list of tables and queries it times out after 30 seconds. and shows it was last cached in June 2019. When I try on a different machine but connecting to the same database it says the cache has not been refreshed since 2014!
It appears to me that Access queries that use the "Nz()" function will NOT appear in the list of queries available in Alteryx. This was the specific situation for me. Nz() is an Access-specific function, and that may be the problem. I have not tested the visibility situation with queries that use other functions besides Nz(). So, for your queries that are not appearing in Alteryx's list, check to see if it is using any function at all. That may be the culprit.