Illustrator :: Making Changes To Design Files

I'm having an issue with the save feature in Illustrator CS5.5 (15.1.0 for mac). Typically when making changes to design files, we will save the Illustrator file first, then save as a PDF proof to send to the client. Our issue is that the file appears to save correctly, but when opening the Illustrator document a few days later, we find that only SOME of the changes were saved. Now keep in mind that I've only saved the document once, why would only a few changes save from one single save point?
 
On top of this, our PDFs come out without any problems, and all changes save just fine.
 
This is a major issue for us, as we need to be able to trust that ALL previous changes save, as we use the Illustrator document to create subsequent versions. We don't have the time to check through every minute detail to make sure that the file saved properly. This should be a very basic function of the program, yet it is creating big time headaches for us.
 
Could it be that we are saving as PDF first, then as AI? Would that somehow affect the ability of Illustrator to save properly?