When the User Directory is synchronized and a user cannot be found, the user is automatically deactivated.
This article covers how to avoid RootAdmins being deactivated from changes done to the LDAP filters used to query users with the User Directory Connector.
Note that you cannot intentionally deactivate a RootAdmin where the user has been set to Delete prohibited. To deactivate the RootAdmin user, first clear the Delete prohibited selection.
For details see Inactivating users (Help.com).
If it is too late, take a look at Admin Account Disabled After LDAP Filter Added
Make sure the rootAdmin accounts used are not excluded with the LDAP Filter implemented. For steps on how to test LDAP Fiters prior to using in Qlik Sense see Qlik Sense on Windows: Configuring and testing LDAP filters for User Directory Connector
As an additional measure, the following may be performed: