500 GB Drive to Terra and Back

Hello,
I have a terabyte that I use at the office to save everything. I also have a 500gb "portable" drive that I travel with. The problem that I am running into is updating the files. The terabyte is used by others and files are "updated" on certain projects. When I return, other projects are updated on my portable drive. I ran a small file set (10MB) on both drives and tried to "sync" them with "Equalize". Some files were modified and or deleted in one drive and other files were modified or deleted in the other drive. This did not work! Apparently, it sync'd one way, deleted files in destination and did check if a new file existed in destination before deleting.
In short, Delete File A in Source and modified File A in Destination. When it sync'd, File A was deleted. Is there a way of "flagging" when a file is deleted vs if a file is updated? I ran this test because I had a corrupt file once and deleted it from the source (had a back up on the destination). When I sync'd, the file was deleted (had an extra copy on my flash drive for a presentation)