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For things like PuTTY that do have an installer, you can use Company Portal and set an application as Available vs. Assigned. I agree with you for apps that do not have an installer (i.e. the Sysinternals suite) that I would like a good way to drop these standalone files.
I think, he is talking about syncing problem for some executable file on OneDrive only.
I've the same issue to, without finding a solution, to permit sync without using a huge daily network bandwidth.