Views:
Question:
Is it possible to have multiple AD Sync V2 configurations on a single machine?

Answer:
By product design, the User Sync Tool has to be executed in the domain where you want to synchronize users from. Nonetheless, you may set up several ADSync tools as long as it is set up on different machines (only one configuration per machine). The ADSync tool can only have one active configuration file (C:\ProgramData\ADSync\ADSyncConfiguration.xml). This means that when executed as a scheduled task, it will always load the same configuration file. Additionally, please be aware that it is not possible to configure several separate tasks for one instance of the tool (On one machine or per installation).

Workaround:
Alternatively, it is possible to have two different configuration files and exchange them manually (by changing the name). Once you have exchanged the configuration file, run the tool. If you want to run the User Sync as a scheduled task, this is not possible, and you will have to run it on two different machines.
 
Note: Users must belong to a group that is being synchronized in order not to be deactivated. If you find that users are being deactivated when the other configuration is run, please create a new group to be synced in Active Directory and place the users into that group as well.
 
KBA is applicable to both Cloud & On-premise Organizations.