I believe that the refresh of your object in the microflow forces Mendix to check the required validations on your current screen regardless of the object. You could try putting the required validation in a save or close microflow, that way it wont be triggered with the refresh.
On all actions buttons there is a setting called 'abort on validation errors' that might also be causing this? The refresh shouldn't necessarily cause the required field popup.
Every action button that triggers a microflow has the option 'abort on validation errors' when this is set to Yes the microflow will not execute as long as there are required fields missing from a page. This way you can built your custom save button and still use form validation fields.
Obviously when building a custom delete button on a nested datagrid it doesn't make sense to validate the dataview in your current page, for those cases you can turn of this option by switching it to no.
You'll find this setting in the 'Edit Microflow Settings' popup. See also: https://world.mendix.com/display/refguide6/Starting+Microflows#StartingMicroflows-Abortonvalidationerrors