I have a hard time understanding the difference between the meaning of the check-in link and and the update link in the Components pane of Software Manager. My current suspicion is that a check-in will merely make the component available on the server and will not be pushed out to clients if you haven't configured your product to auto update that is.
Will update check-in the product as well and push out to all clients that have the product installed?
To add to that, if you, for example, check in a newer version of the agent and use the update option to overwrite the existing package, then your deployment task will need to be updated to choose the new version. However, since the clients already have that assigned task, when they invoke it, they will pull the package that is in that same branch, so yes, they may get updated. If you check it into a different branch and not overwrite existing package, it will not affect your existing task.
Now with patches, such as vse or ens, that is a different story. Refer to KB77063 for how to prevent prematurely deploying patches and other updates.
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