How do I know if it is the file being updated? Since it could just be the item properties.
I don't think there is an easy way.
One approach you could take would be to create a hidden field on the document library that stores an MD5 hash of the file contents (set by the event receiver) and then when the item updated event occurs, compare the stored hash against the hash of the current file contents. If they are different, then the file has changed, and you would update the stored hash with the new hash.
Having said that, this probably won't work with MS Office documents, since whenever you update the SharePoint properties of a word doc for example, the properties are also written into the content of the document, thus changing the file.