I created a new “save-as” skp file. After working in this new file I opened the original file and found that everything I had deleted in the new “save-as” file had also been deleted in the original file.
What the heck Sketchup?!?!?
By any chance are you using a file storage / synchronization service like Drive, Dropbox, OneDrive and the like?
or perhaps you failed to “save as” in a different name?