I was going to remove an AD Forest from AD Connect and took for granted that this would be an easy operation to do from within the AD Connect wizard.
I realized that it is just possible to add AD Forests. I than thought that miisclient would be the place to do this. There is two solution to this that I know off.
1. Uninstall and reinstall AC Connect.
The other that I prefer is described here.
Disable the AD Sync Scheduler by running this PowerShell command:
Import-Module ADSync Set-AdsyncScheduler -SyncCycleEnabled $false
The next step is to open Synchronization Service (miisclient) located in the install directory of Microsoft Azure AD Sync. By default, this is C:\Program Files\Microsoft Azure AD Sync\UIShell\miisclient.exe. Once you have it opened, click on the Connectors tab, then right click on the connector for the forest that you want to remove, and click “Delete”
You will then be prompted, asking if you want to just delete the Connector Space, or delete the Connector and the Connector Space. The former option removes all data, but keeps the configuration in case you want to use it again later. The latter option deletes the data and the configuration. This option should only be used if you don’t plan on syncing the forest again.
Now you just need to re-enable the AD Sync Scheduler with this cmdlet:
Set-ADSyncScheduler -SyncCycleEnabled $true
Good luck with the config.