the structure its name is the same as before. The change is just the name of the variable of the used structure.
This should not make any problems while compiling. Sometimes old project settings are changed also concerning to file extensions which are changed with new installation. If you delete your <projectname>.sc file in the .metadata folder it may solve some issues of compiling. But close your workspace and eclipse before deleting. After restart of the eclipse that file will be created.
If you have other compile errors please describe. I did all the time the updates to newer version and I never had big problems.
which FX3 SDK you used before?