In Eclipse, CVS text comparing works poorly against large numbers of difference between the local and the remote version. It's very desirable to update the the status of comparison every once in a while by a simple command. Basically it's reloading the local file, do the comparison again, to see where we have reached, and try not to make mistakes.
Unfortunately, "Team" - "Synchronize" again after editing every several lines is not convenient, neither does it solve our problem. As I have observed, when there are many differences, Eclipse can mark the already identical lines as different to the remote ones, if we use this approach to compare again.
How can we solve it in Eclipse?
At last I found a simple enough solution, but can be ignored easily: use the "Java structure compare" panel.
Re-"Synchronize" will mess the whole file up, so don't do it in the middle, unless you are at the final stage and have fewer enough differences.
Just a little piece of humble opinion about how to use Eclipse more efficiently. After all it's our daily tool. Better to learn these tricks as soon as possible.