I had couple of issue removing a partition on apacheds. It seems that if you do not perform the operations in the right order you could crash you server and it would not start again. Here are the steps I performs to successfully remove a partition.
Remove the organization node
Connect to the configuration panel
Go to the advanced partition editor
Remove the partition
Delete the indexes on the partion:
Restart the server.
It should be ok
Connect from command line:
ldapsearch -x -H ldap://localhost:10399 -D"uid=admin,ou=system" -wXXXXX -s sub "(cn=Soullard)" -LLL +
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