When you are upgrading a server or moving datbases, you should apply some maintenance to the Notes databases.
The simple way to do this is to ahve a cmd file (or batch file), that runs the necessary commands to fix the databases.
nfixup -L -F -Y %1
ncompact -D -c -i  -n -v -ZU %1 
nupdall -R %1 
nupdall -X %1 
Running these commands (or batch file) script with the Domino server down has the advantage that you can fix the Domino Directory (NAMES>NSF) as well.
On R8.5 you need to have CREATE_R85_DATABASES=1 in the NOTES.INI.
On 9.0, you need to have CREATE_R9_DATABASES=1 in the NOTES.INI.

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