Solidworks custom toolbox copies rolling back in assembly

So I am trying to make a custom clock design and I have made a few custom pieces. I opened the part for a toolbox rack and then saved it as a copy before I edited it. Then I flexed it into a half circle and added some mating holes. When I loaded it up back into the assembly everything was fine. But as soon as I closed the assembly and part and reopened the assembly it reversed my custom changes to the rack and even changed the name to the original rack compared to my named saved copy. Is there something I'm doing wrong? Is there a way to take a toolbox part and customize it as a separate copy and have it still work.

Also side note if you move a file after having it in an assembly is there anyway to help solidworks find that moved part or do you just have to delete it and re add it from its new file location?