This is just information for others that may have had a similar issue.
When developing a Custom PBI Visual, I added a new property (which was to be invisible - but visible or invisible - the same issue occured). Running 'pbiviz start' i.e debugging, the property worked fine and as expected. It could be saved and reloaded but when I ran 'pbiviz package', the persisted property value disappeared when saved and reverted to default.
After, much effort, I finally realised that the package needed a new GUID which can be created in a new directory running 'pbiviz new'. Take the generated GUID from that pbiviz.json and paste it into the pbiviz.json file of the original app.
Whether this is a known problem or it only happens for me, I really don't know! But FYI, this is how I fixed it.
