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I want to subscribe atlassian access so my end-users and agents can have SSO and login with windows account.
As per my understanding, end users are free and agents are paid (jira service management/jira software).
We've found a huge number of end-users that have been registered an account in trello free.
I've already contacted all, and most of them are not using it so most of the accounts can be deleted.
atlassian access will charge me on those users with trello free license, when in fact they are endusers of my instance.
This is a huge pain for many users unfortunately. To answer to your questions
Is there any way to separate products from atlassian access and SSO?
No you can't separate them.
If not, is there any way that I can delete the trello accounts not in use?
Deleting a trello account you must read this: https://support.atlassian.com/trello/docs/deleting-your-trello-account/
However I think that you can simply deactivate the account if you don't want to be charged. You can't delete your trello account, if that user has an atlassian account.
There is an open issue an currently in progress about this. Vote and watch it https://jira.atlassian.com/browse/CLOUD-11072