perhaps you could carry the thousands over into a new score set starting at 1 and use them as a separate display set 'on the front' of the first 999? I admit this is not ideal, but it might save you from losing your complete score system within your current set up.
Just to note that its not just that, the timer in my game is now displaying crazy decimals such as 7.6500001 or 29.65000002 when I just have a simple counter going up .05 every .05, I sent an email to the bugs team but they haven't responded yet...Hopefully it means they are working on a fix
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kipper
Also, GameSalad gets confused around 100 Billion.