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Could you please give a try with the suggestions listed here and let us know your observations
You can query database and find the entries which are not required based on the database agents you see on UI.
1) Navigate to <controller-install-dir>/bin folder
2) For windows
3) mysql> select * from machine_instance;
Once you find the entries that needs to be cleaned up on UI.
4) Please execute the query like
update machine_instance set mark_for_delete=1 AND historical=1 where name LIKE '%db%';
I gave a sample query for matching names that starts with db. Please give the names accordingly. Once you set mark_for_delete as 1, it will clean up the entries on UI. Please wait for few mins say 2-3 for the entries to be disappeared from UI.
please make sure those db agent java processes are no longer in reporting state by killing those process. Otherwise they will reregister and get settled on UI.
Please let us know if you still face any issues.
If this doesn't work, then its a product limitation.