If you are using SRM with storage replication, it depends on how much time storage array might take time to change the direction of replication.
If you are using SRM with vSphere replication, it depends on checksum tasks while pointing back to existing disks at PR site.
In either of these scenarios, we can't really estimate the time it might take. It all depends on a lot of factors and may vary from environment to environment. For ex: Data changes, network, no.of VMs, datastore's,etc. Rest assured, running VMs are not affected when you run re-protect.
It makes sense, if our environment is powerful enough and not being bogged down due to performance issues.