Many of us have shifted the development of AEM from CRXDE to Eclipse since Adobe have released its first version of eclipse plugin. Since its a first version, it does have some issues with the sync especially with exporting project from eclipse to the server. Sling IDE have already done a fix but we might have to wait for the next release of AEM developer tool to get this fix officially.
As I got help from this community, I have tried to put in notes on the same to have a patch over the existing AEM developer tool till its release. Do refer the same