Hi I dont understand what a ccProject actually does when you save it. Every time I save one it never actually keeps any data, if i open the saved file it just opens up the default character.
I have been using ccAvatar to save my projects because it actually works, am i missing something?

Have not used cc3 since it came out because of the lack of the appearance editor but what you describe is definetely not the way it should work, the basic difference between the two formats is that a ccproject retains all the edits you made to the avatar (morph slider values) and keeps the textures editable, basically all the substance parameters can be recalled, the iavatar format bakes the substances as a texture and the morph sliders values are lost. So basically it is meant as a final output format like flattening a psd when exported as jpeg, the image is there but you no longer have access to the layers.

You are not missing anything something is conflicting with cc3, things you can try:

Use save as instead of save
Launch cc3 as administrator
Momentarily disable the antivirus real time protection
Check that you have proper permissions for the folder/drive you are saving to. A quick way of checking this is to try to save a text file, using notepad, in that location if you dont have the proper permissions an error will occur ( i consider this less likely to be the case since apparently you can save avatar files, but is worth checking it out in case the other suggestions fail)