The specifics are a little unclear, but here are some options.
Consider saving them to a mat file with a unique filename. However, they will still contain the same variable names, so when loaded back into the workspace, will replace any existing variables with the same names.
You could return them through the function output. That allows you to assign them to variables with whatever name you want, allowing you to have both at the same time.
If there are a lot of variables, consider using a structure so you only have to pass out one variable.