Usually with software update delays devices won't show any updates within that 90 day period so the user cannot manually install the update.
I don't know what happens if you command devices to update via the dashboard but I would assume if should still fail.
I would verify that the devices have indeed got the software update restriction applied. You can do the via the settings page in your Meraki dashboard and clicking on the settings, it will then show the install status for the devices that the policy applies to.
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