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Ayush, I don't use Public so I don't know if this will work, but try changing the measures you don't want to show to dimensions. This should take them off your Measure Name list. Then when you need them you can change them back.
Also, the un-hiding of hidden fields when publishing to Public doesn't sound like expected behavior to me, but again I don't know public. You might want to talk to support.
For a separate data source, I have 2 type of measures, I need 1 type each in 2 separate graphs. So, putting them into dimensions may not be the best of options. Since I need to have global filter operating on them, I need to have only 1 connection.
Any other way to reduce filter the contents of the filter?