I don't know if this would work as a bit of a solution to the upgrade problem if you added and moved the additional fields to another table.
There is currently an import feature but not an export. If users could export their current entries and then import them into the new table.
The only other solution is as you say to start fresh. With most that may not be a problem for the data. If they can keep all of their settings they can then delete just the data if they don't need it. Not a clean solution but that might be the only other option.
The biggest advantage of moving the fields to a separate table would be giving user's an unlimited number fields. The other advantage since I personally, at least at this point in time, use any additional fields is I wouldn't have an Extra field 1 and field 2 in the window when adding an event.
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