Unfortunately, it will depend on what is causing the problem. I have had syncing problems recently because I change the name of some collections using calibre. The issue was that I changed the case of some of the collection names. One went from from "reading" to "Reading". That caused problems because I ended up with two collections instead of one and the syncing didn't handle that properly. If I had done the rename on the device, it would have been OK. Add that I have multiple devices syncing and it got into a loop.
The fix was to manually deleted all the troublesome collections on one device, and then do a sync. That worked with no issues. And I was able to do several syncs. Then I went through each of the devices and did syncs on all of them. After that I was calibre created the desired collections and syncing has been working with no problems.
I found this by looking at the logs the device produce. I have developers mode turned on with the logging for sync and SQL enabled. Then I needed to telnet into the device and use logread to watch the log. I have read these logs a lot over the years and this error did jump out as it was repeated a lot of times.
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