Prototype corruption over time

Hi Everyone, It seems to me when I go back to my prototypes after some time (a few months) to see if any improvements can be made, the prototype I created is not the same anymore. It seems as if it’s been corrupted in some way and I have to fix many parts of it. I have copied and pasted things from the original file into a special prototype file (to help with loading times) and the two files do not match anymore. Has anyone had the same issues? It becomes a big deal when linking to prototypes from a portfolio.