Every time I open up an assembly, Solidworks ask me to find the missing files. I have used selected them time and time again but it doesn't seem to stick for some reason. I've also clicked file > open > click once on the file > references > and edited all of these to the right location but it still does not seem to know where the heck to get the files from for the assembly. Help please.
After fixing the assembly, do you save it? Are the missing parts in read only sub-assemblies?
Assuming you've saved the Assembly after re-linking the files and it still has problems, you might try getting all the references squared away and then doing a Pack and Go to a new location (or in the same location with new names). That should refresh all the references. See How can I create a new Assembly or Drawing similar to an existing one? if you aren't familiar with it.
In system options under External References, uncheck the "Exclude active folders and recent save locations" - 
Hi Abraham,
When you move files around, are you using SolidWorks Explorer to do it?
As a first suggestion, I would go into SolidWorks Explorer and use this to ensure that ALL of the files required are where they should be. Do NOT use ordinary Windows File Explorer to move SolidWorks files.
Secondly, if by chance in trying to correct this issue you have opened an individual file and then tried "save as" to a new folder, you will still have the original copy sitting in the old folder.
Dave.