Hi @Garrett_Wade
Great questions and great thoughts.
First off - I think a workaround would be to export your file from your hub as a .f3z file and then uploading it via the data panel. I would try that when you receive the error and see if it will repair it. This is not an ideal solution, but it might provide a workaround in the meantime.
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This would lead to another question. Besides using 'Save as' rather than save right now due to this being known to potentially cause issues (possibly my problem here). Should I also stop work on other designs built in this same manner or continue with them under the understanding that i'm at risk of having to redo it?
This is a great question. First to clarify: "File -> Save As" is broken. Right clicking the component and selecting "Save Copy As" is functional.
If it were me, I would probably perform a "save copy as" on any misbehaving components and re-derive them - particularly if the original component and the "saved as" component are derived into the same file. I've seen this cause some issues. But if you haven't seen issues relating to that (unexplained/unexpected de-linking or requesting link be updating) you may not have to worry about it.
Another question for you - are you an admin on both computers?