After going through multiple iterations of trying to get my project admins to dismiss the warning message, and failing, yet again, I found this comment on JSDSERVER-1256 which has resolved my problem .

jean-francois.forget2020484362 added a comment - 28/Jul/2020 4:06 PM
Alexander Wechsler I think you can fix this from the JSD configuration page (https://your.jira.domain/secure/admin/SDConfiguration.jspa).
Set "Permission scheme error" to "Yes, don't show non-critical permission scheme warnings to project administrators."

Thank you jean-francois.forget2020484362

Please, Please, PLEASE can something be done about this?

A new Jira administrator has just been added and guess what? Yes, through no fault of his own he's clicked the wrong button! I've now got to change the permission scheme back and go through the pain of ensuring ALL 27 admins click the "Dismiss" link again 

In case anyone else is wondering how to identify which JIRA Admins have dismissed the error and which have yet to do so, this is the reply I received from Atlassian:

Whenever an admin dismisses a permission scheme configuration warning message in Service Desk project e.g. about Delete Issue permission, record such as the following is added to AO_54307E_CAPABILITY table:

CAPABILITY_NAME	CAPABILITY_VALUE	ID	SERVICE_DESK_ID	USER_KEY
DISMISS_WARNING_FOR_PERMISSION_SCHEME_10201_com.atlassian.servicedesk.internal.permission.misconfiguration.error.TeamRoleMissingRecommendedPermissionsWarning_DELETE_ISSUES	true	10	3	admin

 • The record mentions the relevant permission scheme and the user key of the admins who have dismissed the warnings.
• Any admins who have no record on this table for their user key obviously haven't clicked the dismiss button.
• But once any admin clicks the upgrade button to fix the scheme, the record will be updated and CAPABILITY_VALUE will change to false for all admins who previously dismissed this message.

@MatthewMcMahon - Do you know if there is a way to identify in the database, or somewhere else, which Jira Administrators have dismissed the error and which have yet to do so?

I've come across this issue for a 2nd time (see my comment dated 5th May 2016 for the 1st!)

This time, I am trying to limit the Assignable user to only be members of a specified group picker field. I can easily change the permission scheme, but I face the same problem with getting all JIRA admin to dismiss the warning (and then any new admin, added at any time in the future, to dismiss it too).

I attempted my 2016 change 4 or 5 times before giving up trying to coax everyone to click "Dismiss this warning". I can't imagine it will be any easier this time around, hence, we'll have to live without the desired configuration yet again

I see that the error message has changed slightly, but it still hints that the error should be "fixed" by clicking the "Upgrade permission scheme" button. 

We highly appreciate if this feature can be implemented soon. This is very important to us. The point to note is, imagine a situation where a system admin ignores such "fix this" warning once, and if the same same warning appeaser for users in below privilege level (ex: Project admins) it is contradictory to what is required. Because a system admin has already decided not to fix that issue as it is the expected level of permission granted.

Although this ticket was raised off the back off a suggestion I made, I just wanted to add another comment as I am having great difficulty removing the "service-desk-agent" delete issue permissions which should be a simple task to do. Despite sending several very clear emails and reminders to all of my JIRA administrators (of which there are more than I'd like, due to the tasks that they need to perform being locked down to admin only), the change has been reversed by different administrators both times I have made the change.
I believe that the problem is that the error that is displayed makes people believe that there is a real problem and makes it obvious how to "fix" it and less obvious how to ignore the warning. This is great if there is a real problem, but in my case there isn't!

I would like to suggest that, when this error message is shown:
1) the wording is amended from "Some problems need your attention..." to "Some problems may need your attention..."
2) it would be great if a message that stands out can be added to the error message by the person that makes the change to the permission scheme (e.g. something like "Please dismiss this warning - I have made a change to remove "delete issues" permission from service-desk-agents. If you click on the "Upgrade permission scheme" button, then you will reverse the changes that are required")
3) it would be great if the error message showed a list of who had already dismissed the warning (as that would make people more likely to dismiss the warning themselves, rather than thinking that they have to "fix" the problem as they are the one receiving the error)