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12.2.1.2 Enterprise Manager inaccurate and very slow after shutdown

Hi all
Our server that hosts the BI environment went down (unexpectedly) and ever since then everything has been causing issues.
To begin with, restarting services took a few hours (it normally takes under 20 minutes) and was possible only after I reset the boot.properties file.
Then Enterprise Manager is very slow to log in to and shows servers as down, when in fact they are all up (We are able to log into analytics and run reports, albeit very very slowly)
Also, I have lost credentials for all the users, except weblogic and even the normal BI groups like BI Consumer etc are not visible under console.
Any ideas?