If you are using FlexDeploy 5.42.0.1 or lower version, see Project Security.
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If there are many Groups in your FlexDeploy installation, you can use the Filter option to limit displayed groups, but when you click Save, all changes are applied irrespective of Filtered display data. For example, if you select values for one group and then filter to find another group and update it's its settings and then you click Save, changes for both groups will be saved.
At any point, if you decide to inherit permissions from parent again, then click Revert to Defaults and click Save.
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