I remember having to manually refresh design on the Domino Directory. Make sure you have a backup copy of the database so you can restore any views/agents that you have added/ltered for you environment (I sorted all the views and agents by “last modified by” and blocked template updates on anything we had changed prior to refreshing the design). Forms should not be blocked from changing.
It is not too late to run utilities. They should be run from a command prompt when the Domino service is not running. You can run multiple threads against specific groups (folders) of databases to make it go faster. We found that we could run about 6 threads. After that, the CPU utilization got too high.