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When you say you removed the battery for 30 minute intervals, did the device do a hard reset? If it didn't do a hard reset, you might want to try that but be aware that you will lose data and installed programs since it will revert back to factory state. Also, did you check to see if you have any alarms and notifications going off? That may be the cause of the flashing green light.
As for your sync issue, I don't think there's a way to sync from SD or CF card. Have you tried using the built-in backup utility? It can be found under Programs - Data Backup. It's not a great utility and is prone to failure (in my experience), but it's worth a shot and better than losing all your data (if it works).
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