Thanks for the help. Yes, I insist on using LDD. I tried Stud.io and couldn't even figure out how to zoom in and out. Though I still don't understand how all these groups were created? I didn't make them! Was it somehow from importing models? Maybe I was holding the wrong key?
I deleted all the groups rezipped the two files. There were over 2000 groups all the same, some with subgroups, that were
<Group transformation="1,0,0,0,1,0,0,0,1,0,0,0" pivot="0,0,0" partRefs=""/>
I must have messed something up because after rezipping it says, "Unable to load file Unable to open file" in LDD. I couldn't open the .lxfml with LDD either. It says, "Untitled" in the window bar and there is nothing there. Must be my LDD version is too old and outdated.