Your CR2 files are the same today as they were when you first installed Lightroom. Your Lightroom catalogue stores all the settings you've changed for each file.
If you delete the JPGs from that folder the only thing that will happen is that you delete the JPGs. Your RAW files will still be there, and Lightroom will still have the list of all the changes you've made to each one stored in the catalogue.
Just be sure that you ARE deleting the JPGs and not the CR2 files. Are you planning to do this from a windows explorer type window or from within Lightroom?
If you plan to do something similar in future, you might want to export to a different folder and uncheck the option to "include exported files in catalogue" which is on the export panel somewhere.