JDS replication is driven from the child nodes. If a child node is setup to replicate from a parent node, and the parent node has a package available that the child node "wants", it will start downloading it the next time it checks in.
If you don't want to replicate "now", due to a one-time something big changing like what you had, you can make sure that no JDS nodes have your root JDS listed as a parent. The child nodes won't see new packages on their parents, which will suspend replication. To start them replicating, just revert your changes. You can also mark certain/all packages as unwanted on a child node by editing the child node and setting "Files to Replicate" to "Specific Files". You can then add in files over time to take some manual control over this replication.
If you're just trying to conserve bandwidth, you can "Limit [the] Download Rate" on specific JDS child nodes. This is static, per child node, but you can specify a "safe" replication speed so that it doesn't adversely affect network utilization.
If you really want to limit all replication to specific times of day, rather than throttling it but replicating all of the time, you can edit the crontab on the server. Right now it's set to check in, and replicate any packages, every 5 minutes. With some fancy editing of the crontab, you could take control over this. But note, this is fully unsupported by JAMF and the new installer will most likely overwrite, or otherwise mangle, your modifications. I would try this in a test environment first, and watch what happens during an upgrade, so you can be prepared for what you can expect if you move this to production.
