As mentioned in the question, I often encounter the situation shown in the picture below: Problems demonstrate

I'm using the Clean... directive here, not the Reconcile Offline Work...directive Clean...

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Samwise On

This bug was fixed in the server in release 2016.2:

https://www.perforce.com/perforce/doc.current/user/relnotes.txt

    #1382996 (Job #74886, #86396) **
        'p4 clean' would fail to sync files when needed when they
        are exclusively opened by another client. This has been
        fixed.

Double check that you're on release 2016.2+ of the server; if you are, you should be at the very least be able to use p4 clean as a workaround (e.g. by adding it as a custom tool to P4V).